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Naghizadeh MM, Bakhshandeh B, Noorbakhsh F, Yaghmaie M, Masoudi-Nejad A. Rewiring of miRNA-mRNA bipartite co-expression network as a novel way to understand the prostate cancer related players. Syst Biol Reprod Med 2023:1-12. [PMID: 37018429 DOI: 10.1080/19396368.2023.2187268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
The differential expression and direct targeting of mRNA by miRNA are two main logics of the traditional approach to constructing the miRNA-mRNA network. This approach, could be led to the loss of considerable information and some challenges of direct targeting. To avoid these problems, we analyzed the rewiring network and constructed two miRNA-mRNA expression bipartite networks for both normal and primary prostate cancer tissue obtained from PRAD-TCGA. We then calculated beta-coefficient of the regression-model when miR was dependent and mRNA independent for each miR and mRNA and separately in both networks. We defined the rewired edges as a significant change in the regression coefficient between normal and cancer states. The rewired nodes through multinomial distribution were defined and network from rewired edges and nodes was analyzed and enriched. Of the 306 rewired edges, 112(37%) were new, 123(40%) were lost, 44(14%) were strengthened, and 27(9%) weakened connections were discovered. The highest centrality of 106 rewired mRNAs belonged to PGM5, BOD1L1, C1S, SEPG, TMEFF2, and CSNK2A1. The highest centrality of 68 rewired miRs belonged to miR-181d, miR-4677, miR-4662a, miR-9.3, and miR-1301. SMAD and beta-catenin binding were enriched as molecular functions. The regulation was a frequently repeated concept in the biological process. Our rewiring analysis highlighted the impact of β-catenin and SMAD signaling as also some transcript factors like TGFB1I1 in prostate cancer progression. Altogether, we developed a miRNA-mRNA co-expression bipartite network to identify the hidden aspects of the prostate cancer mechanism, which traditional analysis -like differential expression- was not detect it.
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Affiliation(s)
- Mohammad Mehdi Naghizadeh
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Behnaz Bakhshandeh
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Marjan Yaghmaie
- Hematology, Oncology and Stem Cell Transplantation Research Center, Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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2
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Zhang C, Wu J, Chen Q, Tan H, Huang F, Guo J, Zhang X, Yu H, Shi W. Allosteric binding on nuclear receptors: Insights on screening of non-competitive endocrine-disrupting chemicals. ENVIRONMENT INTERNATIONAL 2022; 159:107009. [PMID: 34883459 DOI: 10.1016/j.envint.2021.107009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) can compete with endogenous hormones and bind to the orthosteric site of nuclear receptors (NRs), affecting normal endocrine system function and causing severe symptoms. Recently, a series of pharmaceuticals and personal care products (PPCPs) have been discovered to bind to the allosteric sites of NRs and induce similar effects. However, it remains unclear how diverse EDCs work in this new way. Therefore, we have systematically summarized the allosteric sites and underlying mechanisms based on existing studies, mainly regarding drugs belonging to the PPCP class. Advanced methods, classified as structural biology, biochemistry and computational simulation, together with their advantages and hurdles for allosteric site recognition and mechanism insight have also been described. Furthermore, we have highlighted two available strategies for virtual screening of numerous EDCs, relying on the structural features of allosteric sites and lead compounds, respectively. We aim to provide reliable theoretical and technical support for a broader view of various allosteric interactions between EDCs and NRs, and to drive high-throughput and accurate screening of potential EDCs with non-competitive effects.
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Affiliation(s)
- Chi Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Jinqiu Wu
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Qinchang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Haoyue Tan
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Fuyan Huang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Jing Guo
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Wei Shi
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China.
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Wang L, Lei Y, Gao Y, Cui D, Tang Q, Li R, Wang D, Chen Y, Zhang B, Wang H. Association of finasteride with prostate cancer: A systematic review and meta-analysis. Medicine (Baltimore) 2020; 99:e19486. [PMID: 32282699 PMCID: PMC7220188 DOI: 10.1097/md.0000000000019486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The Prostate Cancer Prevention Trial has shown a protective effect of finasteride on prostate cancer, but it also showed that finasteride can increase the risk of high-grade prostate cancer. Several studies have investigated the relationship between finasteride and prostate cancer, but these studies have shown inconsistent results. ETHICS The protocol was approved by the institutional review board of each study center. Written informed consent will be obtained from all patients before registration, in accordance with the Declaration of Helsinki. METHODS We performed a systematic literature review and meta-analysis to assess the association between finasteride and prostate cancer. Systematic literature searches were conducted using PubMed, EMBASE, Science Direct/Elsevier, MEDLINE, CNKI, and the Cochrane Library up to October 2018 to identify studies that involved the relationship between finasteride and prostate cancer. Meta-analysis was performed using Review Manager and Stata software. Combined ORs were identified with 95% confidence intervals (95% CI) in a random or fixed effects model. RESULTS Eight studies were identified, including 54,335 cases of patients that used finasteride and 9197 patients who served as placebo controls. Our results illustrate that there is a significant correlation between finasteride use and prostate cancer with combined ORs of 0.70 [0.51, 0.96]. A significant correlation between finasteride use and high-grade prostate cancer was also observed with combined ORs of 2.10 [1.85, 2.38]. CONCLUSIONS This study confirms that finasteride significantly reduced the risk of prostate cancer; however, the malignant degree of prostate cancer was increased. Studies with larger sample sizes are needed to better clarify the correlation between finasteride use and prostate cancer.
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4
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Senapati D, Kumari S, Heemers HV. Androgen receptor co-regulation in prostate cancer. Asian J Urol 2019; 7:219-232. [PMID: 32742924 PMCID: PMC7385509 DOI: 10.1016/j.ajur.2019.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/30/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PCa) progression relies on androgen receptor (AR) action. Preventing AR's ligand-activation is the frontline treatment for metastatic PCa. Androgen deprivation therapy (ADT) that inhibits AR ligand-binding initially induces remission but eventually fails, mainly because of adaptive PCa responses that restore AR action. The vast majority of castration-resistant PCa (CRPC) continues to rely on AR activity. Novel therapeutic strategies are being explored that involve targeting other critical AR domains such as those that mediate its constitutively active transactivation function, its DNA binding ability, or its interaction with co-operating transcriptional regulators. Considerable molecular and clinical variability has been found in AR's interaction with its ligands, DNA binding motifs, and its associated coregulators and transcription factors. Here, we review evidence that each of these levels of AR regulation can individually and differentially impact transcription by AR. In addition, we examine emerging insights suggesting that each can also impact the other, and that all three may collaborate to induce gene-specific AR target gene expression, likely via AR allosteric effects. For the purpose of this review, we refer to the modulating influence of these differential and/or interdependent contributions of ligands, cognate DNA-binding motifs and critical regulatory protein interactions on AR's transcriptional output, which may influence the efficiency of the novel PCa therapeutic approaches under consideration, as co-regulation of AR activity.
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Affiliation(s)
| | - Sangeeta Kumari
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA
| | - Hannelore V Heemers
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA.,Department of Urology, Cleveland Clinic, Cleveland, OH, USA.,Department of Hematology/Medical Oncology, Cleveland Clinic, Cleveland, OH, USA
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6
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Zamagni A, Cortesi M, Zanoni M, Tesei A. Non-nuclear AR Signaling in Prostate Cancer. Front Chem 2019; 7:651. [PMID: 31616657 PMCID: PMC6775214 DOI: 10.3389/fchem.2019.00651] [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: 04/19/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
Despite the key role played by androgen receptor (AR) in tumor cell aggressiveness and prostate cancer (PCa) progression, its function in the tumor microenvironment (TME) is still controversial. Increasing studies highlight the crucial role played by TME modulation in treatment outcome and tumor cell spreading. In this context, targeting specific constituents of the TME could be considered an alternative approach to classic treatments directed against cancer cells. Currently, androgen deprivation therapy (ADT) is a routinely adopted strategy in the management of PCa, with initial success, and consecutive fail. A possible justification to this is the fact that ADT aims to target all the transcription/translation-related activities of AR, which are typical of tumor epithelial cells. Less is still known about side effects of ADT on TME. Cancer Associated Fibroblasts (CAFs), for example, express a classic AR, mostly confined in the extra-nuclear portion of the cell. In CAFs ADT exerts a plethora of non-transcriptional effects, depending by the protein partner linked to AR, leading to cell migration, proliferation, and differentiation. In recent years, substantial progress in the structure-function relationships of AR, identification of its binding partners and function of protein complexes including AR have improved our knowledge of its signaling axis. Important AR non-genomic effects and lots of its cytoplasmatic binding partners have been described, pointing out a fine control of AR non-genomic pathways. Accordingly, new AR inhibitors have been designed and are currently under investigation. Prompt development of new approaches to target AR or block recruitment of its signaling effectors, or co-activators, is urgently needed. The present review takes an in-depth look at current literature, furnishing an exhaustive state-of-the-art overview of the non-genomic role of AR in PCa, with particular emphasis on its involvement in TME biology.
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Affiliation(s)
- Alice Zamagni
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), IRCCS, Meldola, Italy
| | - Michela Cortesi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), IRCCS, Meldola, Italy
| | - Michele Zanoni
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), IRCCS, Meldola, Italy
| | - Anna Tesei
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), IRCCS, Meldola, Italy
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Agbo L, Lambert JP. Proteomics contribution to the elucidation of the steroid hormone receptors functions. J Steroid Biochem Mol Biol 2019; 192:105387. [PMID: 31173874 DOI: 10.1016/j.jsbmb.2019.105387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
Abstract
Steroid hormones have far-ranging biological impacts and more are continuously being uncovered. Over the last decades, proteomics approaches have become key to better understand biological processes. Due to multiple technical breakthroughs allowing for the concurrent identification and/or quantification of thousands of analytes using mass spectrometers, researchers employing proteomics tools today can now obtain truly holistic views of multiple facets of the human proteome. Here, we review how the field of proteomics has contributed to discoveries about steroid hormones, their receptors and their impact on human pathologies. In particular, the involvement of steroid receptors in cancer initiation, development, metastasis and treatment will be highlighted. Techniques at the forefront of the proteomics field will also be discussed to present how they can contribute to a better understanding of steroid hormone receptors.
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Affiliation(s)
- Lynda Agbo
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Québec, QC, Canada; Research Center CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Québec, QC, Canada; Research Center CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada.
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8
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Shamilov R, Aneskievich BJ. Intrinsic Disorder in Nuclear Receptor Amino Termini: From Investigational Challenge to Therapeutic Opportunity. NUCLEAR RECEPTOR RESEARCH 2019. [DOI: 10.32527/2019/101417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Rambon Shamilov
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092, USA
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9
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Sivoňová MK, Kaplán P, Tatarková Z, Lichardusová L, Dušenka R, Jurečeková J. Androgen receptor and soy isoflavones in prostate cancer. Mol Clin Oncol 2018; 10:191-204. [PMID: 30680195 DOI: 10.3892/mco.2018.1792] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/16/2018] [Indexed: 12/13/2022] Open
Abstract
Androgens and androgen receptor (AR) play a critical role not only in normal prostate development, but also in prostate cancer. For that reason, androgen deprivation therapy (ADT) is the primary treatment for prostate cancer. However, the majority of patients develop castration-resistant prostate cancer, which eventually leads to mortality. Novel therapeutic approaches, including dietary changes, have been explored. Soy isoflavones have become a focus of interest because of their positive health benefits on numerous diseases, particularly hormone-related cancers, including prostate and breast cancers. An important strategy for the prevention and/or treatment of prostate cancer might thus be the action of soy isoflavones on the AR signaling pathway. The current review article provides a detailed overview of the anticancer potential of soy isoflavones (genistein, daidzein and glycitein), as mediated by their effect on AR.
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Affiliation(s)
- Monika Kmetová Sivoňová
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Peter Kaplán
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.,Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Zuzana Tatarková
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Lucia Lichardusová
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Róbert Dušenka
- Department of Urology, Jessenius Faculty of Medicine and UHM in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Jana Jurečeková
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia
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Bakuchiol exhibits anti-metastasis activity through NF-κB cross-talk signaling with AR and ERβ in androgen-independent prostate cancer cells PC-3. J Pharmacol Sci 2018; 138:1-8. [DOI: 10.1016/j.jphs.2017.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 04/18/2017] [Accepted: 04/28/2017] [Indexed: 12/11/2022] Open
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11
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Eukaryotic transcription factors: paradigms of protein intrinsic disorder. Biochem J 2017; 474:2509-2532. [DOI: 10.1042/bcj20160631] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022]
Abstract
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.
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12
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Kulkarni P. Intrinsically disordered proteins and prostate cancer: pouring new wine in an old bottle. Asian J Androl 2017; 18:659-61. [PMID: 27427556 PMCID: PMC5000785 DOI: 10.4103/1008-682x.184272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Prakash Kulkarni
- Protein Biophysics & Structural Biology Laboratory, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
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