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Guo S, Ding R, Zhao Q, Wang X, Lv S, Ji XY. Recent Insights into the Roles of PEST-Containing Nuclear Protein. Mol Biotechnol 2024:10.1007/s12033-024-01188-5. [PMID: 38762838 DOI: 10.1007/s12033-024-01188-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 04/26/2024] [Indexed: 05/20/2024]
Abstract
PEST-containing nuclear protein (PCNP), a short-lived small nuclear protein with 178 amino acids, is a nuclear protein containing two PEST sequences. PCNP is highly expressed in several malignant tumors such as cervical cancer, rectal cancer, and lung cancer. It is also associated with cell cycle regulation and the phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) and Wnt signaling pathways during tumor growth. The present article discuss how PCNP regulates the PI3K/AKT/mTOR and Wnt signaling pathways and related proteins, and the ubiquitination of PCNP regulates tumor cell cycle as well as the progress of the application of PCNP in the pathophysiology and treatment of colon cancer, human ovarian cancer, thyroid cancer, lung adenocarcinoma and oral squamous cell carcinoma. The main relevant articles were retrieved from PubMed, with keywords such as PEST-containing nuclear protein (PCNP), cancer (tumor), and signaling pathways as inclusion/exclusion criteria. Relevant references has been included and cited in the manuscript.
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Affiliation(s)
- Shiyun Guo
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Ruidong Ding
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Qian Zhao
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Xu Wang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Shuangyu Lv
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, 475004, Henan, China.
| | - Xin-Ying Ji
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, 475004, Henan, China.
- Kaifeng Key Laboratory for Infectious Diseases and Biosafety, Kaifeng, 475004, Henan, China.
- Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Mazhai, Erqi District, Zhengzhou, 450064, Henan, China.
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2
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Li X, Xiong H, Mou X, Huang C, Thomas ER, Yu W, Jiang Y, Chen Y. Androgen receptor cofactors: A potential role in understanding prostate cancer. Biomed Pharmacother 2024; 173:116338. [PMID: 38417290 DOI: 10.1016/j.biopha.2024.116338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
Prostate cancer (PCa) is witnessing a concerning rise in incidence annually, with the androgen receptor (AR) emerging as a pivotal contributor to its growth and progression. Mounting evidence underscores the AR's ability to recruit cofactors, influencing downstream gene transcription and thereby fueling the proliferation and metastasis of PCa cells. Although, clinical strategies involving AR antagonists provide some relief, managing castration resistant prostate cancer (CRPC) remains a formidable challenge. Thus, the need of the hour lies in unearthing new drugs or therapeutic targets to effectively combat PCa. This review encapsulates the pivotal roles played by coactivators and corepressors of AR, notably androgen receptor-associated protein (ARA) and steroid receptor Coactivators (SRC) in PCa. Our data unveils how these cofactors intricately modulate histone modifications, cell cycling, SUMOylation, and apoptosis through their interactions with AR. Among the array of cofactors scrutinised, such as ARA70β, ARA24, ARA160, ARA55, ARA54, PIAS1, PIAS3, SRC1, SRC2, SRC3, PCAF, p300/CBP, MED1, and CARM1, several exhibit upregulation in PCa. Conversely, other cofactors like ARA70α, PIASy, and NCoR/SMRT demonstrate downregulation. This duality underscores the complexity of AR cofactor dynamics in PCa. Based on our findings, we propose that manipulating cofactor regulation to modulate AR function holds promise as a novel therapeutic avenue against advanced PCa. This paradigm shift offers renewed hope in the quest for effective treatments in the face of CRPC's formidable challenges.
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Affiliation(s)
- Xiang Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Haojun Xiong
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xingzhu Mou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China; Department of Dermatology, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Cancan Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China; Department of Dermatology, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | | | - Wenjing Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Yu Jiang
- The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China.
| | - Yan Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China; Department of Dermatology, The Affiliated Hospital, Southwest Medical University, Luzhou, China.
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3
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Balraj AS, Muthamilselvan S, Raja R, Palaniappan A. PRADclass: Hybrid Gleason Grade-Informed Computational Strategy Identifies Consensus Biomarker Features Predictive of Aggressive Prostate Adenocarcinoma. Technol Cancer Res Treat 2024; 23:15330338231222389. [PMID: 38226611 PMCID: PMC10793196 DOI: 10.1177/15330338231222389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/18/2023] [Accepted: 12/06/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Prostate adenocarcinoma (PRAD) is a common cancer diagnosis among men globally, yet large gaps in our knowledge persist with respect to the molecular bases of its progression and aggression. It is mostly indolent and slow-growing, but aggressive prostate cancers need to be recognized early for optimising treatment, with a view to reducing mortality. METHODS Based on TCGA transcriptomic data pertaining to PRAD and the associated clinical metadata, we determined the sample Gleason grade, and used it to execute: (i) Gleason-grade wise linear modeling, followed by five contrasts against controls and ten contrasts between grades; and (ii) Gleason-grade wise network modeling via weighted gene correlation network analysis (WGCNA). Candidate biomarkers were obtained from the above analysis and the consensus found. The consensus biomarkers were used as the feature space to train ML models for classifying a sample as benign, indolent or aggressive. RESULTS The statistical modeling yielded 77 Gleason grade-salient genes while the WGCNA algorithm yielded 1003 trait-specific key genes in grade-wise significant modules. Consensus analysis of the two approaches identified two genes in Grade-1 (SLC43A1 and PHGR1), 26 genes in Grade-4 (including LOC100128675, PPP1R3C, NECAB1, UBXN10, SERPINA5, CLU, RASL12, DGKG, FHL1, NCAM1, and CEND1), and seven genes in Grade-5 (CBX2, DPYS, FAM72B, SHCBP1, TMEM132A, TPX2, UBE2C). A RandomForest model trained and optimized on these 35 biomarkers for the ternary classification problem yielded a balanced accuracy ∼ 86% on external validation. CONCLUSIONS The consensus of multiple parallel computational strategies has unmasked candidate Gleason grade-specific biomarkers. PRADclass, a validated AI model featurizing these biomarkers achieved good performance, and could be trialed to predict the differentiation of prostate cancers. PRADclass is available for academic use at: https://apalania.shinyapps.io/pradclass (online) and https://github.com/apalania/pradclass (command-line interface).
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Affiliation(s)
- Alex Stanley Balraj
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Sangeetha Muthamilselvan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Rachanaa Raja
- Department of Pharmaceutical Technology, UCE, Anna University (BIT campus), Trichy, India
| | - Ashok Palaniappan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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4
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Salehi T, Callisto A, Beecher MB, Hissaria P. Tofacitinib as a biologic response modifier in VEXAS syndrome: A case series. Int J Rheum Dis 2023; 26:2340-2343. [PMID: 37337622 DOI: 10.1111/1756-185x.14785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/22/2023] [Accepted: 06/03/2023] [Indexed: 06/21/2023]
Affiliation(s)
- Tania Salehi
- Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Alicia Callisto
- Central Adelaide Local Health Network, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mark Brian Beecher
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Pravin Hissaria
- Central Adelaide Local Health Network, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
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Gong Z, Zhang H, Ge Y, Wang P. Long noncoding RNA MIAT regulates TP53 ubiquitination and expedites prostate adenocarcinoma progression by recruiting TBL1X. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119527. [PMID: 37356458 DOI: 10.1016/j.bbamcr.2023.119527] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
Despite recent advances in cancer immunotherapy, their efficacy for treating patients with prostate adenocarcinoma (PRAD) is low due to complex immune evasion mechanisms. However, the function of long non-coding RNA (lncRNAs) in immune evasion has not been fully clarified. This study aimed to expound the role of myocardial infarction-associated transcript (MIAT), a lncRNA significantly upregulated in three PRAD-associated datasets, in immune evasion and try to reveal the potential mechanism. MIAT was highly expressed in PRAD tissues and predicted poor prognosis, and suppression of MIAT inhibited the malignant biological behavior of PRAD cells. Moreover, the depletion of MIAT promoted the immune response of CD8+ T cells and hampered the immune evasion of PRAD cells. In addition, MIAT downregulated TP53 protein expression by recruiting transducin beta-like protein 1X (TBL1X) for ubiquitination modification. Silencing of TP53 or overexpression of TBL1X was enough to abate the tumor suppressive effects of MIAT knockdown in vitro and in vivo. Our results provide evidence for a novel regulation mechanism of CD8+ T cells in PRAD and MIAT may serve as a potential therapeutic target in PRAD.
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Affiliation(s)
- Zheng Gong
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, PR China
| | - Huijing Zhang
- Department of Endoscopy, The First Affiliated Hospital of China Medical University, Shenyang, PR China
| | - Yuntian Ge
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, PR China
| | - Peng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, PR China.
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6
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Development of strategies for community engaged research dissemination by basic scientists: a case study. Transl Res 2023; 252:91-98. [PMID: 36108910 DOI: 10.1016/j.trsl.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 01/14/2023]
Abstract
As depicted in the translational research continuum, dissemination of research findings to past research participants and the community-at-large is integral to improving health outcomes. Blocks in translation exist in which poor dissemination is a major contributor. Limited progress has been made on how to engage basic scientists at T1 and T2 phases to meaningfully disseminate study findings to community. Our objective is to report on 4 cases of community engaged research dissemination activities among 3 basic scientists (ie, a cancer biologist, a biochemist, and a molecular biologist.): a townhall, a radio listening session, a community newsletter, and a Facebook Live segment. The Meharry Community Engagement Core dissemination team designed these activities using community informed processes. To plan and conduct these activities, a basic scientist is partnered with a community engaged researcher and a community-based organization to create a dissemination product which can be understood and potentially used by past research participants and the community-at-large. We share reflections from basic scientists, community organizations, and event participants. Finally, we provide competencies, informed by basic scientists, needed to engage in effective, community-engaged research dissemination. The activities, reflections, and competencies can be used by basic scientists and academic institutions as models to guide their community engaged research dissemination activities. This work supports the goal to bridge the translational research gap.
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7
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Androgen Receptor Signaling Inhibition in Advanced Castration Resistance Prostate Cancer: What Is Expected for the Near Future? Cancers (Basel) 2022; 14:cancers14246071. [PMID: 36551557 PMCID: PMC9776956 DOI: 10.3390/cancers14246071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The androgen signaling pathway is the cornerstone in the treatment of high risk or advanced prostate cancer patients. However, in recent years, different mechanisms of resistance have been defined in this field, limiting the efficacy of the currently approved antiandrogen drugs. Different therapeutic approaches are under research to assess the role of combination therapies against escape signaling pathways or the development of novel antiandrogen drugs to try to solve the primary or acquired resistance against androgen dependent or independent pathways. The present review aims to summarize the current state of androgen inhibition in the therapeutic algorithm of patients with advanced prostate cancer and the mechanisms of resistance to those available drugs. In addition, this review conducted a comprehensive overview of the main present and future research approaches in the field of androgen receptor inhibition to overcome these resistances and the potential new drugs under research coming into this setting.
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8
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Zhang F, Zheng H, Xian Y, Song H, Wang S, Yun Y, Yi L, Zhang G. Profiling Substrate Specificity of the SUMO Protease Ulp1 by the YESS–PSSC System to Advance the Conserved Mechanism for Substrate Cleavage. Int J Mol Sci 2022; 23:ijms232012188. [PMID: 36293045 PMCID: PMC9603560 DOI: 10.3390/ijms232012188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
SUMO modification is a vital post-translational regulation process in eukaryotes, in which the SUMO protease is responsible for the maturation of the SUMO precursor and the deconjugation of the SUMO protein from modified proteins by accurately cleaving behind the C-terminal Gly–Gly motif. To promote the understanding of the high specificity of the SUMO protease against the SUMO protein as well as to clarify whether the conserved Gly–Gly motif is strictly required for the processing of the SUMO precursor, we systematically profiled the specificity of the S. cerevisiae SUMO protease (Ulp1) on Smt3 at the P2–P1↓P1’ (Gly–Gly↓Ala) position using the YESS–PSSC system. Our results demonstrated that Ulp1 was able to cleave Gly–Gly↓ motif-mutated substrates, indicating that the diglycine motif is not strictly required for Ulp1 cleavage. A structural-modeling analysis indicated that it is the special tapered active pocket of Ulp1 conferred the selectivity of small residues at the P1–P2 position of Smt3, such as Gly, Ala, Ser and Cys, and only which can smoothly deliver the scissile bond into the active site for cleavage. Meanwhile, the P1’ position Ala of Smt3 was found to play a vital role in maintaining Ulp1’s precise cleavage after the Gly–Gly motif and replacing Ala with Gly in this position could expand Ulp1 inclusivity against the P1 and P2 position residues of Smt3. All in all, our studies advanced the traditional knowledge of the SUMO protein, which may provide potential directions for the drug discovery of abnormal SUMOylation-related diseases.
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Affiliation(s)
- Faying Zhang
- School of Life Sciences, Hubei University, Wuhan 430062, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hui Zheng
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yufan Xian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haoyue Song
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Shengchen Wang
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yueli Yun
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Li Yi
- School of Life Sciences, Hubei University, Wuhan 430062, China
- Correspondence: (L.Y.); (G.Z.)
| | - Guimin Zhang
- School of Life Sciences, Hubei University, Wuhan 430062, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (L.Y.); (G.Z.)
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9
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Gomarasca M, Lombardi G, Maroni P. SUMOylation and NEDDylation in Primary and Metastatic Cancers to Bone. Front Cell Dev Biol 2022; 10:889002. [PMID: 35465332 PMCID: PMC9020829 DOI: 10.3389/fcell.2022.889002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/25/2022] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications comprise series of enzymatically-driven chemical modifications, virtually involving the entire cell proteome, that affect the fate of a target protein and, in turn, cell activity. Different classes of modifications can be established ranging from phosphorylation, glycosylation, ubiquitination, acetylation, methylation, lipidation and their inverse reactions. Among these, SUMOylation and NEDDylation are ubiquitin-like multi-enzymatic processes that determine the bound of SUMOs and NEDD8 labels, respectively, on defined amino acidic residues of a specific protein and regulate protein function. As fate-determinants of several effectors and mediators, SUMOylation and NEDDylation play relevant roles in many aspects of tumor cell biology. Bone represents a preferential site of metastasis for solid tumors (e.g., breast and prostate cancers) and the primary site of primitive tumors (e.g., osteosarcoma, chondrosarcoma). Deregulation of SUMOylation and NEDDylation affects different aspects of neoplastic transformation and evolution such as epithelial-mesenchymal transition, adaptation to hypoxia, expression and action of tumor suppressors and oncogenic mediators, and drug resistance. Thereby, they represent potential therapeutic targets. This narrative review aims at describing the involvement and regulation of SUMOylation and NEDDylation in tumor biology, with a specific focus on primary and secondary bone tumors, and to summarize and highlight their potentiality in diagnostics and therapeutic strategies.
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Affiliation(s)
- Marta Gomarasca
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
- Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Polska
- *Correspondence: Giovanni Lombardi,
| | - Paola Maroni
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
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10
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Elmarakeby HA, Hwang J, Arafeh R, Crowdis J, Gang S, Liu D, AlDubayan SH, Salari K, Kregel S, Richter C, Arnoff TE, Park J, Hahn WC, Van Allen EM. Biologically informed deep neural network for prostate cancer discovery. Nature 2021; 598:348-352. [PMID: 34552244 PMCID: PMC8514339 DOI: 10.1038/s41586-021-03922-4] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 08/17/2021] [Indexed: 12/20/2022]
Abstract
The determination of molecular features that mediate clinically aggressive phenotypes in prostate cancer remains a major biological and clinical challenge1,2. Recent advances in interpretability of machine learning models as applied to biomedical problems may enable discovery and prediction in clinical cancer genomics3-5. Here we developed P-NET-a biologically informed deep learning model-to stratify patients with prostate cancer by treatment-resistance state and evaluate molecular drivers of treatment resistance for therapeutic targeting through complete model interpretability. We demonstrate that P-NET can predict cancer state using molecular data with a performance that is superior to other modelling approaches. Moreover, the biological interpretability within P-NET revealed established and novel molecularly altered candidates, such as MDM4 and FGFR1, which were implicated in predicting advanced disease and validated in vitro. Broadly, biologically informed fully interpretable neural networks enable preclinical discovery and clinical prediction in prostate cancer and may have general applicability across cancer types.
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Affiliation(s)
- Haitham A Elmarakeby
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Al-Azhar University, Cairo, Egypt
| | - Justin Hwang
- University of Minnesota, Division of Hematology, Oncology and Transplantation, Minneapolis, MN, USA
| | - Rand Arafeh
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jett Crowdis
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sydney Gang
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Liu
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saud H AlDubayan
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Keyan Salari
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven Kregel
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Taylor E Arnoff
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jihye Park
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eliezer M Van Allen
- Dana-Farber Cancer Institute, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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Zinatizadeh MR, Schock B, Chalbatani GM, Zarandi PK, Jalali SA, Miri SR. The Nuclear Factor Kappa B (NF-kB) signaling in cancer development and immune diseases. Genes Dis 2021; 8:287-297. [PMID: 33997176 PMCID: PMC8093649 DOI: 10.1016/j.gendis.2020.06.005] [Citation(s) in RCA: 202] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 05/26/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023] Open
Abstract
The nuclear factor kappa B (NF-kB) family of transcription factors plays an essential role as stressors in the cellular environment, and controls the expression of important regulatory genes such as immunity, inflammation, death, and cell proliferation. NF-kB protein is located in the cytoplasm, and can be activated by various cellular stimuli. There are two pathways for NF-kB activation, as the canonical and non-canonical pathways, which require complex molecular interactions with adapter proteins and phosphorylation and ubiquitinase enzymes. Accordingly, this increases NF-kB translocation in the nucleus and regulates gene expression. In this study, the concepts that emerge in different cellular systems allow the design of NF-kB function in humans. This would not only allow the development for rare diseases associated with NF-kB, but would also be used as a source of useful information to eliminate widespread consequences such as cancer or inflammatory/immune diseases.
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Affiliation(s)
| | - Bettina Schock
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, BT7 1NN, United Kingdom
| | - Ghanbar Mahmoodi Chalbatani
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, 1336616357, Iran
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, 1336616357, Iran
| | | | - Seyed Amir Jalali
- Department of Medical Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 1336616357, Iran
| | - Seyed Rouhollah Miri
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, 1336616357, Iran
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12
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García-Olivares M, Romero-Córdoba S, Ortiz-Sánchez E, García-Becerra R, Segovia-Mendoza M, Rangel-Escareño C, Halhali A, Larrea F, Barrera D. Regulation of anti-tumorigenic pathways by the combinatory treatment of calcitriol and TGF-β in PC-3 and DU145 cells. J Steroid Biochem Mol Biol 2021; 209:105831. [PMID: 33582304 DOI: 10.1016/j.jsbmb.2021.105831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 02/07/2023]
Abstract
Calcitriol and transforming growth factors beta (TGF-β) are involved in several biological pathways such as cell proliferation, differentiation, migration and invasion. Their cellular effects could be similar or opposite depending on the genetic target, cell type and context. Despite the reported association of calcitriol deficiency and disruption of the TGF-β pathway in prostate cancer and the well-known independent effects of calcitriol and TGF-βs on cancer cells, there is limited information regarding the cellular effects of calcitriol and TGF-β in combination. In this study, we in vitro analyze the combinatory effects of calcitriol and TGF-β on cell growth and apoptosis using PC-3 and DU145 human prostate cancer cell lines. Using high-throughput microarray profiling of PC-3 cells upon independent and combinatory treatments, we identified distinct transcriptional landscapes of each intervention, with a higher effect established by the combinatorial treatment, following by TGF-β1 and later by calcitriol. A set of genes and enriched pathways converge among the treatments, mainly between the combinatory scheme and TGF-β1, but the majority were treatment-specific. Of note, CYP24A1, IGFBP3, CDKN1A, NOX4 and UBE2D3 were significantly up-regulated upon the combinatorial treatment whereas CCNA1, members of the CT45A and APOBEC3 family were down-regulated. By public RNA signatures, we were able to confirm the regulation by the co-treatment over cell proliferation and cell cycle. We finally investigated the possible clinical impact of genes modulated by the combinatorial treatment using benchmark prostate cancer data. This comprehensive analysis reveals that the combinatory treatment impairs cell growth without affecting apoptosis and their combinatory actions might synergize and improved their individual effects to reprogram prostate cancer signaling.
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Affiliation(s)
- Mitzi García-Olivares
- Departamento de Biología de la Reproducción "Dr. Carlos Gual Castro", Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Col. Belisario Domínguez, Sección XVI, Ciudad de México, 14080, México
| | - Sandra Romero-Córdoba
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, México; Departamento de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Col. Belisario Domínguez, Sección XVI, Ciudad de México, 14080, México
| | - Elizabeth Ortiz-Sánchez
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Secretaría de Salud, Ciudad de México, México
| | - Rocío García-Becerra
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Mariana Segovia-Mendoza
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510, México
| | - Claudia Rangel-Escareño
- Laboratorio de Genómica Computacional y Biología Integrativa, Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Ciudad de México, 14610, México; Departamento de Ingeniería y Ciencias, Tecnológico de Monterrey, Epigmenio González 500, Soriana, 76140 Santiago de Querétaro, Qro. México
| | - Ali Halhali
- Departamento de Biología de la Reproducción "Dr. Carlos Gual Castro", Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Col. Belisario Domínguez, Sección XVI, Ciudad de México, 14080, México
| | - Fernando Larrea
- Departamento de Biología de la Reproducción "Dr. Carlos Gual Castro", Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Col. Belisario Domínguez, Sección XVI, Ciudad de México, 14080, México
| | - David Barrera
- Departamento de Biología de la Reproducción "Dr. Carlos Gual Castro", Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Col. Belisario Domínguez, Sección XVI, Ciudad de México, 14080, México.
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13
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Liu Z, Liu C, Yan K, Liu J, Fang Z, Fan Y. Huaier Extract Inhibits Prostate Cancer Growth via Targeting AR/AR-V7 Pathway. Front Oncol 2021; 11:615568. [PMID: 33708629 PMCID: PMC7940541 DOI: 10.3389/fonc.2021.615568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/07/2021] [Indexed: 01/05/2023] Open
Abstract
The androgen receptor (AR) plays a pivotal role in prostatic carcinogenesis, and it also affects the transition from hormone sensitive prostate cancer (HSPC) to castration-resistant prostate cancer (CRPC). Particularly, the persistent activation of the androgen receptor and the appearance of androgen receptor splicing variant 7 (AR-V7), could partly explain the failure of androgen deprivation therapy (ADT). In the present study, we reported that huaier extract, derived from officinal fungi, has potent antiproliferative effects in both HSPC and CRPC cells. Mechanistically, huaier extract downregulated both full length AR (AR-FL) and AR-V7 mRNA levels via targeting the SET and MYND domain-containing protein 3 (SMYD3) signaling pathway. Huaier extract also enhanced proteasome-mediated protein degradation of AR-FL and AR-V7 by downregulating proteasome-associated deubiquitinase ubiquitin-specific protease 14 (USP14). Furthermore, huaier extract inhibited AR-FL/AR-V7 transcriptional activity and their nuclear translocation. More importantly, our data demonstrated that huaier extract could re-sensitize enzalutamide-resistant prostate cancer cells to enzalutamide treatment in vitro and in vivo models. Our work revealed that huaier extract could be effective for treatment of prostate cancer either as monotherapy or in combination with enzalutamide.
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Affiliation(s)
- Zhengfang Liu
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China
| | - Cheng Liu
- Department of Urology, Peking University Third Hospital, Beijing, China
| | - Keqiang Yan
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China
| | - Jikai Liu
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China.,Department of Medicine, Center for Molecular Medicine (CMM) and Bioclinicum, Karolinska Institute and Karolinska University Hospital Solna, Solna, Sweden
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China
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14
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Samaržija I. Post-Translational Modifications That Drive Prostate Cancer Progression. Biomolecules 2021; 11:247. [PMID: 33572160 PMCID: PMC7915076 DOI: 10.3390/biom11020247] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 02/07/2023] Open
Abstract
While a protein primary structure is determined by genetic code, its specific functional form is mostly achieved in a dynamic interplay that includes actions of many enzymes involved in post-translational modifications. This versatile repertoire is widely used by cells to direct their response to external stimuli, regulate transcription and protein localization and to keep proteostasis. Herein, post-translational modifications with evident potency to drive prostate cancer are explored. A comprehensive list of proteome-wide and single protein post-translational modifications and their involvement in phenotypic outcomes is presented. Specifically, the data on phosphorylation, glycosylation, ubiquitination, SUMOylation, acetylation, and lipidation in prostate cancer and the enzymes involved are collected. This type of knowledge is especially valuable in cases when cancer cells do not differ in the expression or mutational status of a protein, but its differential activity is regulated on the level of post-translational modifications. Since their driving roles in prostate cancer, post-translational modifications are widely studied in attempts to advance prostate cancer treatment. Current strategies that exploit the potential of post-translational modifications in prostate cancer therapy are presented.
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Affiliation(s)
- Ivana Samaržija
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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15
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K6-linked SUMOylation of BAF regulates nuclear integrity and DNA replication in mammalian cells. Proc Natl Acad Sci U S A 2020; 117:10378-10387. [PMID: 32332162 PMCID: PMC7229763 DOI: 10.1073/pnas.1912984117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Barrier-to-autointegration factor (BAF) is a highly conserved protein in metazoans that has multiple functions during the cell cycle. We found that BAF is SUMOylated at K6, and that this modification is essential for its nuclear localization and function, including nuclear integrity maintenance and DNA replication. K6-linked SUMOylation of BAF promotes binding and interaction with lamin A/C to regulate nuclear integrity. K6-linked SUMOylation of BAF also supports BAF binding to DNA and proliferating cell nuclear antigen and regulates DNA replication. SENP1 and SENP2 catalyze the de-SUMOylation of BAF at K6. Disrupting the SUMOylation and de-SUMOylation cycle of BAF at K6 not only disturbs nuclear integrity, but also induces DNA replication failure. Taken together, our findings demonstrate that SUMOylation at K6 is an important regulatory mechanism that governs the nuclear functions of BAF in mammalian cells.
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16
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Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA. Sci Rep 2020; 10:6190. [PMID: 32277101 PMCID: PMC7148341 DOI: 10.1038/s41598-020-63102-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnosis, prognosis and monitoring treatment of disease. However, a sensitive and specific whole-genome sequencing (WGS) method is required to identify novel genetic variations (i.e., SNVs, CNVs and INDELS) on ccfDNA that can be used as clinical biomarkers. In this article, five WGS methods were compared: ThruPLEX Plasma-seq, QIAseq cfDNA All-in-One, NEXTFLEX Cell Free DNA-seq, Accel-NGS 2 S PCR FREE DNA and Accel-NGS 2 S PLUS DNA. The Accel PCR-free kit did not produce enough material for sequencing. The other kits had significant common number of SNVs, INDELs and CNVs and showed similar results for SNVs and CNVs. The detection of variants and genomic signatures depends more upon the type of plasma sample rather than the WGS method used. Accel detected several variants not observed by the other kits. ThruPLEX seemed to identify more low-abundant SNVs and SNV signatures were similar to signatures observed with the QIAseq kit. Accel and NEXTFLEX had similar CNV and SNV signatures. These results demonstrate the importance of establishing a standardized workflow for identifying non-invasive candidate biomarkers. Moreover, the combination of variants discovered in ccfDNA using WGS has the potential to identify enrichment pathways, while the analysis of signatures could identify new subgroups of patients.
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17
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Lindenmann U, Brand M, Gall F, Frasson D, Hunziker L, Kroslakova I, Sievers M, Riedl R. Discovery of a Class of Potent and Selective Non-competitive Sentrin-Specific Protease 1 Inhibitors. ChemMedChem 2020; 15:675-679. [PMID: 32083799 DOI: 10.1002/cmdc.202000067] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 01/17/2023]
Abstract
Sentrin-specific proteases (SENPs) are responsible for the maturation of small ubiquitin-like modifiers (SUMOs) and the deconjugation of SUMOs from their substrate proteins. Studies on prostate cancer revealed an overexpression of SENP1, which promotes prostate cancer progression as well as metastasis. Therefore, SENP1 has been identified as a novel drug target against prostate cancer. Herein, we report the discovery and biological evaluation of potent and selective SENP1 inhibitors. A structure-activity relationship (SAR) of the newly identified pyridone scaffold revealed allosteric inhibitors with very attractive in vitro ADMET properties regarding plasma binding and plasma stability for this challenging target. This study also emphasizes the importance of biochemical mode of inhibition studies for de novo designed inhibitors.
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Affiliation(s)
- Urs Lindenmann
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Michael Brand
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Flavio Gall
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - David Frasson
- Institute of Chemistry and Biotechnology, Center of Molecular Biology, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Lukas Hunziker
- Institute of Chemistry and Biotechnology, Center of Molecular Biology, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Ivana Kroslakova
- Institute of Chemistry and Biotechnology, Center of Molecular Biology, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Martin Sievers
- Institute of Chemistry and Biotechnology, Center of Molecular Biology, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, ZHAW Zurich University of Applied Sciences, Einsiedlerstr. 31, 8820, Wädenswil, Switzerland
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18
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The Urinary Transcriptome as a Source of Biomarkers for Prostate Cancer. Cancers (Basel) 2020; 12:cancers12020513. [PMID: 32098402 PMCID: PMC7072374 DOI: 10.3390/cancers12020513] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Abstract
Prostate cancer (PCa) is the second most common cancer of men and is typically slow-growing and asymptomatic. The use of blood PSA as a screening method has greatly improved PCa diagnosis, but high levels of false positives has raised much interest in alternative biomarkers. We used next-generation sequencing (NGS) to elucidate the urinary transcriptome of whole urine collected from high-stage and low-stage PCa patients as well as from patients with the confounding diagnosis of benign hyperplasia (BPH). We identified and validated five differentially expressed protein-coding genes (FTH1 BRPF1, OSBP, PHC3, and UACA) in an independent validation cohort of small-volume (1 mL) centrifuged urine (n = 94) and non-centrifuged urine (n = 84) by droplet digital (dd)PCR. These biomarkers were able to discriminate between BPH and PCa patients and healthy controls using either centrifuged or non-centrifuged whole urine samples, suggesting that the urinary transcriptome is a valuable source of non-invasive biomarkers for PCa that warrants further investigation.
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19
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Yang N, Liu S, Qin T, Liu X, Watanabe N, Mayo KH, Li J, Li X. SUMO3 modification by PIAS1 modulates androgen receptor cellular distribution and stability. Cell Commun Signal 2019; 17:153. [PMID: 31752909 PMCID: PMC6868827 DOI: 10.1186/s12964-019-0457-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/10/2019] [Indexed: 01/14/2023] Open
Abstract
Background Abnormal reactivation of androgen receptor (AR) signaling in castration-resistant prostate cancer (CRPC) mainly results from overexpression and down-regulation of AR. Sumoylation of AR can influence its function. However, regulation of AR sumoylation by SUMO E3 ligases PIASs to modify AR distribution and stability are not well understood. Methods We assessed the potential effect of SUMO3 modification on AR intracellular localization by immunostaining in AR-negative prostate cancer DU145 cells, and detected the effect of PIAS1/SUMO3 overexpression on AR sumoylation related degradation. Then we characterized AR sumoylation sites involved modified by SUMO3, and the key residue of PIAS1 involved in itself sumoylation and further mediated AR sumoylation (sumo3-conjugated), translocation and degradation. Finally we detected the recognition of PIAS1 (sumoylation ligase) to MDM2, a ubiquin ligase mediated AR degradation. Results We demonstrate that SUMO E3 ligase PIAS1, along with SUMO3, mediates AR cytosolic translocation and subsequent degradation via a ubiquitin-proteasome pathway. Although AR sumoylation occurs prior to ubiquitination, the SUMO-acceptor lysine 386 on AR, together with ubiquitin-acceptor lysine 845, contribute to PIAS1/SUMO3-induced AR nuclear export, ubiquitination and subsequent degradation. Moreover, PIAS1 itself is modified by SUMO3 overexpression, and mutation of SUMO-acceptor lysine 117 on PIAS1 can impair AR cytoplasmic distribution, demonstrating the essential role of sumoylated PIAS1 in AR translocation. We further determine that sumoylated PIAS1 interacts with AR lysine 386 and 845 to form a binary complex. Consistent with the effect on AR distribution, SUMO3 modification of PIAS1 is also required for AR ubiquitination and degradation by recruiting ubiquitin E3 ligase MDM2. Conclusion Taken together, SUMO3 modification of PIAS1 modulates AR cellular distribution and stability. Our study provided the evidence the crosstalk between AR sumoylation and ubquitination mediated by PIAS1 and SUMO3.
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Affiliation(s)
- Nanyang Yang
- The Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, 5268 People's Street, Changchun, Jilin, 130024, People's Republic of China.,Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Cytology and Genetics, Hengyang School of Medicine, University of South China, Hengyang, Hunan, 421001, People's Republic of China
| | - Sitong Liu
- The Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, 5268 People's Street, Changchun, Jilin, 130024, People's Republic of China.,College of Life Sciences, Jilin University, Changchun, 130012, People's Republic of China
| | - Tian Qin
- The Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, 5268 People's Street, Changchun, Jilin, 130024, People's Republic of China
| | - Xintong Liu
- Dental Hospital, Jilin University, Changchun, 130021, China.,Bioprobe Application Research Unit, RIKEN-Max Planck Joint Research Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan.,Graduate School of Medical & Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nobumoto Watanabe
- Bioprobe Application Research Unit, RIKEN-Max Planck Joint Research Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan.,Graduate School of Medical & Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kevin H Mayo
- Biochemistry, Molecular Biology, and Biophysics, Health Sciences Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jiang Li
- Dental Hospital, Jilin University, Changchun, 130021, China.
| | - Xiaomeng Li
- The Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, 5268 People's Street, Changchun, Jilin, 130024, People's Republic of China.
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20
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Afzal A, Sarfraz M, Li GL, Ji SP, Duan SF, Khan NH, Wu DD, Ji XY. Taking a holistic view of PEST-containing nuclear protein (PCNP) in cancer biology. Cancer Med 2019; 8:6335-6343. [PMID: 31487123 PMCID: PMC6797571 DOI: 10.1002/cam4.2465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/15/2022] Open
Abstract
Polypeptide sequences enriched with proline (P), glutamic acid (E), aspartic acid (D) and serine (S)/ threonine (T) (PEST) have been reported to be the most abundant and frequently distributed at the cellular level. There is growing evidence that PEST sequences act as proteolytic recognition signals for degradation of residual proteins which is critical for activation or deactivation of regulatory proteins involved in cellular signaling pathways of cell growth, differentiation, stress responses and physiological death. A PEST containing nuclear protein (PCNP) was demonstrated as a tumor suppressor in a neuroblastoma cancer model and tumor promoter in lung adenocarcinoma cancer model. Its unique properties like ubiquitination by NIRF, co‐localization with NIRF in nucleus and tumor progression attract the attention of researchers. PCNP was reported to be ubiquitinated by ring finger protein NIRF in E3 ligase manner and as modulator of MAPK and PI3K/AKT/mTOR signaling pathways. In this review, we summarize PCNP linked DNA damage response, Post translational modifications, and transportation to address initiation, prognosis, and resistance of tumor cells in terms of cell cycle regulation, transcription and apoptosis. Hence, we demonstrate PCNP as a novel target in cancer diagnosis and treatment.
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Affiliation(s)
- Attia Afzal
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China.,Faculty of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Muhammad Sarfraz
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China.,Faculty of Pharmacy, The University of Lahore, Lahore, Pakistan.,Muncipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, China
| | - Guang-Lei Li
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China
| | - Shao-Ping Ji
- Muncipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, China
| | - Shao-Feng Duan
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China.,Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Nazeer Hussain Khan
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China
| | - Dong-Dong Wu
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China.,School of Basic Medical Sciences, Henan University College of Medicine, Kaifeng, China
| | - Xin-Ying Ji
- Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, Kaifeng, China.,Kaifeng Key Laboratory of Infection and Biological Safety (KLIBS), Henan University College of Medicine, Kaifeng, China
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21
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Qian S, Zhan X, Lu M, Li N, Long Y, Li X, Desiderio DM, Zhan X. Quantitative Analysis of Ubiquitinated Proteins in Human Pituitary and Pituitary Adenoma Tissues. Front Endocrinol (Lausanne) 2019; 10:328. [PMID: 31191455 PMCID: PMC6540463 DOI: 10.3389/fendo.2019.00328] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/07/2019] [Indexed: 12/30/2022] Open
Abstract
Protein ubiquitination is an important post-translational modification that is associated with multiple diseases, including pituitary adenomas (PAs). Protein ubiquitination profiling in human pituitary and PAs remains unknown. Here, we performed the first ubiquitination analysis with an anti-ubiquitin antibody (specific to K-ε-GG)-based label-free quantitative proteomics method and bioinformatics to investigate protein ubiquitination profiling between PA and control tissues. A total of 158 ubiquitinated sites and 142 ubiquitinated peptides in 108 proteins were identified, and five ubiquitination motifs were found. KEGG pathway network analysis of 108 ubiquitinated proteins identified four statistically significant signaling pathways, including PI3K-AKT signaling pathway, hippo signaling pathway, ribosome, and nucleotide excision repair. R software Gene Ontology (GO) analysis of 108 ubiquitinated proteins revealed that protein ubiquitination was involved in multiple biological processes, cellular components, and molecule functions. The randomly selected ubiquitinated 14-3-3 zeta/delta protein was further analyzed with Western blot, and it was found that upregulated 14-3-3 zeta/delta protein in nonfunctional PAs might be derived from the significantly decreased level of its ubiquitination compared to control pituitaries, which indicated a contribution of 14-3-3 zeta/delta protein to pituitary tumorigenesis. These findings provided the first ubiquitinated proteomic profiling and ubiquitination-involved signaling pathway networks in human PAs. This study offers new scientific evidence and basic data to elucidate the biological functions of ubiquitination in PAs, insights into its novel molecular mechanisms of pituitary tumorigenesis, and discovery of novel biomarkers and therapeutic targets for effective treatment of PAs.
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Affiliation(s)
- Shehua Qian
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaohan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Miaolong Lu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Ying Long
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Dominic M. Desiderio
- The Charles B. Stout Neuroscience Mass Spectrometry Laboratory, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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22
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Chicooree N, Griffiths JR. A Combined Chemical Derivatization/Mass Spectrometric Method for the Enhanced Detection and Relative Quantification of Protein Ubiquitination. Methods Mol Biol 2019; 1977:17-24. [PMID: 30980319 DOI: 10.1007/978-1-4939-9232-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mass spectrometry (MS) is a sensitive analytical technique with wide application across the sciences including for the detection of peptides and proteins in biological analysis. Ubiquitinated (Ub) proteins are typically analyzed by proteolytic digestion and subsequent chromatographic separation followed by MS detection of the resulting isopeptides. Here we describe a novel method which enables enhanced detection of this important posttranslational modification (PTM) by use of a simple chemical labeling strategy prior to Data-Independent Acquisition (DIA) using a SWATH-based acquisition approach on a suitable Quadrupole-Time-Of-Flight (Q-TOF) mass spectrometer.
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23
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Ubiquitination and SUMOylation in the chronic inflammatory tumor microenvironment. Biochim Biophys Acta Rev Cancer 2018; 1870:165-175. [DOI: 10.1016/j.bbcan.2018.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/10/2018] [Accepted: 08/15/2018] [Indexed: 12/28/2022]
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24
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An S, Huang L, Miao P, Shi L, Shen M, Zhao X, Liu J, Huang G. Small ubiquitin-like modifier 1 modification of pyruvate kinase M2 promotes aerobic glycolysis and cell proliferation in A549 human lung cancer cells. Onco Targets Ther 2018; 11:2097-2109. [PMID: 29713182 PMCID: PMC5907896 DOI: 10.2147/ott.s156918] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Objective Lung cancer is the leading cause of cancer-related death worldwide. Aerobic glycolysis is considered the seventh hallmark of cancer. The M2 isoform of pyruvate kinase (PKM2) is an important rate-limiting enzyme in glycolytic pathway, and is strongly expressed in several types of cancer. Thus, understanding the underlying mechanisms of regulation of PKM2 is of great value for targeted therapy for lung cancer. Patients and methods Seventy-three lung adenocarcinoma patients were analyzed in our study. The expression levels of PKM2 were analyzed by immunohistochemistry on tissues. The effect of small ubiquitin-like modifier 1 (SUMO1) on PKM2 expression was investigated using Western blot assay and quantitative polymerase chain reaction. PKM2 SUMO1 modification was determined by in vitro and in vivo SUMOylation assays. 18F-deoxyglucose uptake and lactate production measurements were conducted to research the levels of glycolysis. The level of oxidative phosphorylation in cells was determined by cellular oxygen consumption rate measurements. Cell proliferation assays were carried out to confirm the growth ability of tumor cells. Results PKM2 was overexpressed in lung adenocarcinoma patients based on immunohistochemical staining. Patients with high PKM2 expression had reduced overall survival rate (P=0.017) and disease-free survival rate (P=0.027) compared with those with low PKM2 expression. SUMO1 promoted PKM2-dependent glycolysis. Western blotting analysis showed that SUMO1 knockdown in A549 cells led to a significant decrease in PKM2 protein expression. PKM2 could be covalently modified by SUMO1 at K336 (Lys336) site. SUMO1 modification of PKM2 at Lys-336 site increased glycolysis and promoted its cofactor functions. Moreover, PKM2 SUMO1 modification promoted the proliferation of A549 cells in vitro. Conclusion This information is important in elucidating a new mechanism of regulation of PKM2, and suggested that SUMO1 modification of PKM2 could be a potential therapeutic target in lung cancer.
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Affiliation(s)
- Shuxian An
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liangqian Huang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine & Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Miao
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liang Shi
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mengqin Shen
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoping Zhao
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianjun Liu
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Huang
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine & Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai University of Medicine and Health Sciences, Shanghai, China
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Zou G, Liu T, Guo L, Huang Y, Feng Y, Duan T. MicroRNA‑32 silences WWP2 expression to maintain the pluripotency of human amniotic epithelial stem cells and β islet‑like cell differentiation. Int J Mol Med 2018; 41:1983-1991. [PMID: 29393344 PMCID: PMC5810217 DOI: 10.3892/ijmm.2018.3436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 12/20/2017] [Indexed: 11/06/2022] Open
Abstract
Human amniotic epithelial stem cells (HuAECs) exhibit pluripotent characteristics, which are similar to those of embryonic stem cells, and can differentiate into various adult tissues and cells through directed induction. However, in culture, HuAECs tend to lose their pluripotency, and their directed differentiation capability declines with increasing passage number. The stem cell pluripotency factor octamer-binding protein 4 (Oct4) is an important transcription factor that promotes stem cell self-proliferation and maintains their pluripotency. Previous studies have demonstrated that WW domain containing E3 ubiquitin protein ligase 2 (WWP2) negatively regulates Oct4 expression and stem cell pluripotency. Therefore, the present study aimed to investigate the regulation of WWP2 by microRNAs (miRs), and to evaluate the expression of the downstream factor Oct4 and the maintenance of HuAEC pluripotency. Bioinformatics analysis identified a complementary binding site for miR-32 in the 3′untranslated region of the WWP2 gene, thus suggesting that it may be a target gene of miR-32. Post-infection of HuAECs with a vector overexpressing miR-32, the endogenous expression of WWP2 was significantly decreased, whereas Oct4 expression was significantly increased. Furthermore, miR-32-infected cells differentiated into β islet-like cells by directed induction. The results indicated that after induction, HuAECs overexpressing miR-32 also overexpressed the biomarkers of β islet-like cells. In addition, the ability to secrete insulin was markedly enhanced in response to glucose stimulation, in cells overexpressing miR-32. In conclusion, the present study suggested that miR-32 may effectively inhibit WWP2 expression in HuAECs and promote Oct4 overexpression to maintain their pluripotency.
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Affiliation(s)
- Gang Zou
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200040, P.R. China
| | - Te Liu
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200040, P.R. China
| | - Lihe Guo
- Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P.R. China
| | - Yongyi Huang
- Laboratoire PROTEE, Batiment R, University du Sud Toulon‑Var, 83957 La Garde Cedex, France
| | - Ya Feng
- Department of Neurology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200040, P.R. China
| | - Tao Duan
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200040, P.R. China
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26
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Mallik S, Zhao Z. Towards integrated oncogenic marker recognition through mutual information-based statistically significant feature extraction: an association rule mining based study on cancer expression and methylation profiles. QUANTITATIVE BIOLOGY 2017; 5:302-327. [PMID: 30221015 DOI: 10.1007/s40484-017-0119-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background Marker detection is an important task in complex disease studies. Here we provide an association rule mining (ARM) based approach for identifying integrated markers through mutual information (MI) based statistically significant feature extraction, and apply it to acute myeloid leukemia (AML) and prostate carcinoma (PC) gene expression and methylation profiles. Methods We first collect the genes having both expression and methylation values in AML as well as PC. Next, we run Jarque-Bera normality test on the expression/methylation data to divide the whole dataset into two parts: one that ollows normal distribution and the other that does not follow normal distribution. Thus, we have now four parts of the dataset: normally distributed expression data, normally distributed methylation data, non-normally distributed expression data, and non-normally distributed methylated data. A feature-extraction technique, "mRMR" is then utilized on each part. This results in a list of top-ranked genes. Next, we apply Welch t-test (parametric test) and Shrink t-test (non-parametric test) on the expression/methylation data for the top selected normally distributed genes and non-normally distributed genes, respectively. We then use a recent weighted ARM method, "RANWAR" to combine all/specific resultant genes to generate top oncogenic rules along with respective integrated markers. Finally, we perform literature search as well as KEGG pathway and Gene-Ontology (GO) analyses using Enrichr database for in silico validation of the prioritized oncogenes as the markers and labeling the markers as existing or novel. Results The novel markers of AML are {ABCB11↑∪KRT17↓} (i.e., ABCB11 as up-regulated, & KRT17 as down-regulated), and {AP1S1-∪KRT17↓∪NEIL2-∪DYDC1↓}) (i.e., AP1S1 and NEIL2 both as hypo-methylated, & KRT17 and DYDC1 both as down-regulated). The novel marker of PC is {UBIAD1¶∪APBA2‡∪C4orf31‡} (i.e., UBIAD1 as up-regulated and hypo-methylated, & APBA2 and C4orf31 both as down-regulated and hyper-methylated). Conclusion The identified novel markers might have critical roles in AML as well as PC. The approach can be applied to other complex disease.
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Affiliation(s)
- Saurav Mallik
- Computer Science & Engineering, Aliah University, Newtown, Newtown 700156, India
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Luo Y, You S, Wang J, Fan S, Shi J, Peng A, Yu T. Association between Sumoylation-Related Gene rs77447679 Polymorphism and Risk of Gastric Cancer (GC) in a Chinese Population. J Cancer 2017; 8:3226-3231. [PMID: 29158794 PMCID: PMC5665038 DOI: 10.7150/jca.20587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 08/14/2017] [Indexed: 12/12/2022] Open
Abstract
Purpose: Sumoylation plays a critical role in gene regulation and tumorigenesis, and is hypothesized to correlate with the development of various cancers. So far, there has been no reported association between sumoylation-related genes and the risk of gastric cancer (GC). Methods: A total of 17 tagging single-nucleotide polymorphisms (tag-SNPs) in 5 sumoylation-related genes were selected and genotyped by SNaPshot in a case-control study, including 1021 GC patients and 1304 controls. Odds ratio (OR) and 95% confidential interval (CI) were computed to evaluate the genetic association of the onset of GC. Results: We demonstrated that CBX4 rs77447679 polymorphism was significantly associated with GC risk (P= 0.017; adjusted OR: 1.71; 95% CI: 1.10-2.66). The patients with CC genotype had a lower risk of GC (CC vs. CA+AA, P= 0.017; adjusted OR: 1.24; 95% CI: 1.04-1.49). Conclusion: This study revealed that CBX4 rs77447679 polymorphism was positively associated with GC, and individuals with CC genotype had less risk of GC. The risky effects and functional effect of this polymorphism in GC require further investigation.
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Affiliation(s)
- Ying Luo
- Department of Nephrology & Rheumatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Sihong You
- Department of gastroenterology, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China.,Department of Developmental Genetics, Nanjing Medical University, Nanjing 211166, China
| | - Jirong Wang
- Department of Developmental Genetics, Nanjing Medical University, Nanjing 211166, China.,Department of Oncology, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Shuling Fan
- Department of Nephrology & Rheumatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jie Shi
- Nanjing Red Cross Blood Center, Nanjing 210003, China
| | - Ai Peng
- Department of Nephrology & Rheumatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Tingting Yu
- Department of Developmental Genetics, Nanjing Medical University, Nanjing 211166, China
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Wang L, Song G, Zhang X, Feng T, Pan J, Chen W, Yang M, Bai X, Pang Y, Yu J, Han J, Han B. PADI2-Mediated Citrullination Promotes Prostate Cancer Progression. Cancer Res 2017; 77:5755-5768. [DOI: 10.1158/0008-5472.can-17-0150] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/31/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022]
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Lu H, Li G, Zhou C, Jin W, Qian X, Wang Z, Pan H, Jin H, Wang X. Regulation and role of post-translational modifications of enhancer of zeste homologue 2 in cancer development. Am J Cancer Res 2016; 6:2737-2754. [PMID: 28042497 PMCID: PMC5199751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023] Open
Abstract
Post-translational modifications (PTMs) are critical molecular events which alter protein conformation after their synthesis and diversity protein properties by modulating their stability, localization, interacting partners or the activity of their substrates, consequently exerting pivotal roles in regulating the functions of many important eukaryotic proteins. It has been well acknowledged that PTMs are of great importance in a broad range of biological processes such as gene regulation, cell proliferation, differentiation and apoptosis, tissue development, diseases, tumor progression and drug resistance. As the core and contributing catalytic subunit of Polycomb repressive complex 2(PRC2), Enhancer of zeste homolog 2 (EZH2) is a master epigenetic regulator, often serving as a highly conserved histone methyltransferase (HMTase) to induce histone H3 lysine 27 trimethylation (H3K27me3) and repress gene transcription and expression. Dysregulated EZH2 expression is frequently associated with cancer development and poor prognosis in a wide variety of cancers. Considered its essential role in carcinogenesis, EZH2 is a potential candidate for cancer targeted therapy. Remarkably, mounting evidence highlights that EZH2 expression, activity and stability can be regulated by PTMs including phosphorylation, acetylation, ubiquitination, sumoylation and GlcNAcylation aside from its well-validated modifications in transcriptional and post-transcriptional levels. However, the precise regulatory mechanisms underlying EZH2 PTMs and whether other types of PTMs orchestrate in EZH2 remain largely unclear. In this review, we summarize current advances in the understanding of EZH2 regulation by PTMs and their associated biological functions during tumorigenesis.
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Affiliation(s)
- Haiqi Lu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Guangliang Li
- Department of Medical Oncology, Zhejiang Cancer HospitalHangzhou, Zhejiang, China
| | - Chenyi Zhou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Wei Jin
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Xiaoling Qian
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Zhuo Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
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Jiang W, Sheng C, Gu X, Liu D, Yao C, Gao S, Chen S, Huang Y, Huang W, Fang M. Suppression of Rac1 Signaling by Influenza A Virus NS1 Facilitates Viral Replication. Sci Rep 2016; 6:35041. [PMID: 27869202 PMCID: PMC5116764 DOI: 10.1038/srep35041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 09/13/2016] [Indexed: 11/26/2022] Open
Abstract
Influenza A virus (IAV) is a major human pathogen with the potential to become pandemic. IAV contains only eight RNA segments; thus, the virus must fully exploit the host cellular machinery to facilitate its own replication. In an effort to comprehensively characterize the host machinery taken over by IAV in mammalian cells, we generated stable A549 cell lines with over-expression of the viral non-structural protein (NS1) to investigate the potential host factors that might be modulated by the NS1 protein. We found that the viral NS1 protein directly interacted with cellular Rac1 and facilitated viral replication. Further research revealed that NS1 down-regulated Rac1 activity via post-translational modifications. Therefore, our results demonstrated that IAV blocked Rac1-mediated host cell signal transduction through the NS1 protein to facilitate its own replication. Our findings provide a novel insight into the mechanism of IAV replication and indicate new avenues for the development of potential therapeutic targets.
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Affiliation(s)
- Wei Jiang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunjie Sheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuling Gu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chen Yao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shijuan Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuai Chen
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Yinghui Huang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Wenlin Huang
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou 510060, China
- Key Laboratory of Tumor Targeted Drug in Guangdong Province, Guangzhou Double Bioproducts Co., Ltd., Guangzhou, China
| | - Min Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- International College, University of Chinese Academy of Sciences, Beijing, China
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Lazzarini N, Widera P, Williamson S, Heer R, Krasnogor N, Bacardit J. Functional networks inference from rule-based machine learning models. BioData Min 2016; 9:28. [PMID: 27597880 PMCID: PMC5011349 DOI: 10.1186/s13040-016-0106-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/11/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Functional networks play an important role in the analysis of biological processes and systems. The inference of these networks from high-throughput (-omics) data is an area of intense research. So far, the similarity-based inference paradigm (e.g. gene co-expression) has been the most popular approach. It assumes a functional relationship between genes which are expressed at similar levels across different samples. An alternative to this paradigm is the inference of relationships from the structure of machine learning models. These models are able to capture complex relationships between variables, that often are different/complementary to the similarity-based methods. RESULTS We propose a protocol to infer functional networks from machine learning models, called FuNeL. It assumes, that genes used together within a rule-based machine learning model to classify the samples, might also be functionally related at a biological level. The protocol is first tested on synthetic datasets and then evaluated on a test suite of 8 real-world datasets related to human cancer. The networks inferred from the real-world data are compared against gene co-expression networks of equal size, generated with 3 different methods. The comparison is performed from two different points of view. We analyse the enriched biological terms in the set of network nodes and the relationships between known disease-associated genes in a context of the network topology. The comparison confirms both the biological relevance and the complementary character of the knowledge captured by the FuNeL networks in relation to similarity-based methods and demonstrates its potential to identify known disease associations as core elements of the network. Finally, using a prostate cancer dataset as a case study, we confirm that the biological knowledge captured by our method is relevant to the disease and consistent with the specialised literature and with an independent dataset not used in the inference process. AVAILABILITY The implementation of our network inference protocol is available at: http://ico2s.org/software/funel.html.
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Affiliation(s)
- Nicola Lazzarini
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
| | - Paweł, Widera
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
| | - Stuart Williamson
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Rakesh Heer
- Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
| | - Jaume Bacardit
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
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Lee A, Oh JG, Gorski PA, Hajjar RJ, Kho C. Post-translational Modifications in Heart Failure: Small Changes, Big Impact. Heart Lung Circ 2016; 25:319-24. [PMID: 26795636 PMCID: PMC4775300 DOI: 10.1016/j.hlc.2015.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 12/31/2022]
Abstract
Heart failure is a complex disease process with various aetiologies and is a significant cause of morbidity and death world-wide. Post-translational modifications (PTMs) alter protein structure and provide functional diversity in terms of physiological functions of the heart. In addition, alterations in protein PTMs have been implicated in human disease pathogenesis. Small ubiquitin-like modifier mediated modification (SUMOylation) pathway was found to play essential roles in cardiac development and function. Abnormal SUMOylation has emerged as a new feature of heart failure pathology. In this review, we will highlight the importance of SUMOylation as a regulatory mechanism of SERCA2a function, and its therapeutic potential for the treatment of heart failure.
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Affiliation(s)
- Ahyoung Lee
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jae Gyun Oh
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Przemek A Gorski
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Roger J Hajjar
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Changwon Kho
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, USA.
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Stoehr CG, Walter B, Denzinger S, Ghiorzo P, Sturm RA, Hinze R, Moch H, Junker K, Hartmann A, Stoehr R. The Microphthalmia-Associated Transcription Factor p.E318K Mutation Does Not Play a Major Role in Sporadic Renal Cell Tumors from Caucasian Patients. Pathobiology 2016; 83:165-9. [PMID: 26999813 DOI: 10.1159/000443311] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/14/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The transcription factor MITF (microphthalmia-associated transcription factor) is known to induce expression of hypoxia-inducible factor (HIF1-α), which is involved in renal carcinogenesis. The MITF p.E318K mutation leads to deficient SUMOylation of MITF, resulting in enhanced activation of its target genes. A case-control study on melanoma patients who coincidentally were affected by renal cell carcinoma (RCC) has revealed an elevated risk for mutation carriers to be affected by one or both of these malignancies, suggesting a possible role for MITF p.E318K in renal carcinogenesis. The same study described an MITF mutation frequency of 1.5% in a small cohort of sporadic RCC, but comprehensive data on sporadic renal cell tumors are missing. We therefore tested a large cohort of sporadic renal tumors for MITF p.E318K mutation status. METHODS Genomic DNA was extracted from 426 formalin-fixed, paraffin-embedded sporadic renal tumors that had been graded according to the 2004 WHO classification of renal tumors and staged according to the 2002 TNM classification. The tumor cohort was enriched with papillary and chromophobe RCC, and also contained benign oncocytomas. DNA was tested for MITF p.E318K by pyrosequencing. RESULTS Of 403 analyzable tumors, 402 renal tumors were wild-type ones, and only 1 case showed the MITF p.E318K mutation. This tumor was a clear-cell RCC (pT3b N0 M0 G3 according to the TNM classification 2002). The affected patient was male, 61 years old, and had no known coexisting malignancies. CONCLUSION The MITF p.E318K mutation does not appear to play a major role in sporadic RCC carcinogenesis, but is possibly restricted to a rare subpopulation of inherited RCC.
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Affiliation(s)
- Christine G Stoehr
- Institute of Pathology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
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Serrano-Gomez SJ, Maziveyi M, Alahari SK. Regulation of epithelial-mesenchymal transition through epigenetic and post-translational modifications. Mol Cancer 2016; 15:18. [PMID: 26905733 PMCID: PMC4765192 DOI: 10.1186/s12943-016-0502-x] [Citation(s) in RCA: 506] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/13/2016] [Indexed: 02/07/2023] Open
Abstract
The epithelial to mesenchymal transition (EMT) is a biological process in which a non-motile epithelial cell changes to a mesenchymal phenotype with invasive capacities. This phenomenon has been well documented in multiple biological processes including embryogenesis, fibrosis, tumor progression and metastasis. The hallmark of EMT is the loss of epithelial surface markers, most notably E-cadherin, and the acquisition of mesenchymal markers including vimentin and N-cadherin. The downregulation of E-cadherin during EMT can be mediated by its transcriptional repression through the binding of EMT transcription factors (EMT-TFs) such as SNAIL, SLUG and TWIST to E-boxes present in the E-cadherin promoter. Additionally, EMT-TFs can also cooperate with several enzymes to repress the expression of E-cadherin and regulate EMT at the epigenetic and post- translational level. In this review, we will focus on epigenetic and post- translational modifications that are important in EMT. In addition, we will provide an overview of the various therapeutic approaches currently being investigated to undermine EMT and hence, the metastatic progression of cancer as well.
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Affiliation(s)
- Silvia Juliana Serrano-Gomez
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA, 70112, USA. .,Pontificia Universidad Javeriana, Bogota, Colombia.
| | - Mazvita Maziveyi
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA, 70112, USA.
| | - Suresh K Alahari
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA, 70112, USA.
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Steffen P, Kwiatkowski M, Robertson WD, Zarrine-Afsar A, Deterra D, Richter V, Schlüter H. Protein species as diagnostic markers. J Proteomics 2016; 134:5-18. [DOI: 10.1016/j.jprot.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023]
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Identification of new SUMO activating enzyme 1 inhibitors using virtual screening and scaffold hopping. Bioorg Med Chem Lett 2016; 26:1218-23. [DOI: 10.1016/j.bmcl.2016.01.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/07/2016] [Accepted: 01/12/2016] [Indexed: 11/21/2022]
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The E3 ubiquitin ligase CHIP mediates ubiquitination and proteasomal degradation of PRMT5. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:335-46. [PMID: 26658161 DOI: 10.1016/j.bbamcr.2015.12.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/23/2015] [Accepted: 12/01/2015] [Indexed: 12/12/2022]
Abstract
Protein arginine methyltransferase 5 (PRMT5) is an important member of the protein arginine methyltransferase family that regulates many cellular processes through epigenetic control of target gene expression. Because of its overexpression in a number of human cancers and its essential role in cell proliferation, transformation, and cell cycle progression, PRMT5 has been recently proposed to function as an oncoprotein in cancer cells. However, how its expression is regulated in cancer cells remains largely unknown. We have previously demonstrated that the transcription of PRMT5 can be negatively regulated by the PKC/c-Fos signaling pathway through modulating the transcription factor NF-Y in prostate cancer cells. In the present study, we demonstrated that PRMT5 undergoes polyubiquitination, possibly through multiple lysine residues. We also identified carboxyl terminus of heat shock cognate 70-interacting protein (CHIP), an important chaperone-dependent E3 ubiquitin ligase that couples protein folding/refolding to protein degradation, as an interacting protein of PRMT5 via mass spectrometry. Their interaction was further verified by co-immuoprecipitation, GST pull-down, and bimolecular fluorescence complementation (BiFC) assay. In addition, we provided evidence that the CHIP/chaperone system is essential for the negative regulation of PRMT5 expression via K48-linked ubiquitin-dependent proteasomal degradation. Given that down-regulation of CHIP and overexpression of PRMT5 have been observed in several human cancers, our finding suggests that down-regulation of CHIP may be one of the mechanisms underlying PRMT5 overexpression in these cancers.
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