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Fettweis G, Wagh K, Stavreva DA, Jiménez-Panizo A, Kim S, Lion M, Alegre-Martí A, Rinaldi L, Johnson TA, Gilson E, Krishnamurthy M, Wang L, Ball DA, Karpova TS, Upadhyaya A, Vertommen D, Recio JF, Estébanez-Perpiñá E, Dequiedt F, Hager GL. Transcription factors form a ternary complex with NIPBL/MAU2 to localize cohesin at enhancers. Nucleic Acids Res 2025; 53:gkaf415. [PMID: 40377219 DOI: 10.1093/nar/gkaf415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Revised: 04/14/2025] [Accepted: 05/06/2025] [Indexed: 05/18/2025] Open
Abstract
While the cohesin complex is a key player in genome architecture, how it localizes to specific chromatin sites is not understood. Recently, we and others have proposed that direct interactions with transcription factors lead to the localization of the cohesin-loader complex (NIPBL/MAU2) within enhancers. Here, we identify two clusters of LxxLL motifs within the NIPBL sequence that regulate NIPBL dynamics, interactome, and NIPBL-dependent transcriptional programs. One of these clusters interacts with MAU2 and is necessary for the maintenance of the NIPBL-MAU2 heterodimer. The second cluster binds specifically to the ligand-binding domains of steroid receptors. For the glucocorticoid receptor (GR), we examine in detail its interaction surfaces with NIPBL and MAU2. Using AlphaFold2 and molecular docking algorithms, we uncover a GR-NIPBL-MAU2 ternary complex and describe its importance in GR-dependent gene regulation. Finally, we show that multiple transcription factors interact with NIPBL-MAU2, likely using interfaces other than those characterized for GR.
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Affiliation(s)
- Gregory Fettweis
- Laboratory of Gene Expression and Cancer, GIGA-Molecular & Computational Biology, University of Liège, 4000 Liège, Belgium
| | - Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
| | - Alba Jiménez-Panizo
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
| | - Michelle Lion
- Laboratory of Gene Expression and Cancer, GIGA-Molecular & Computational Biology, University of Liège, 4000 Liège, Belgium
| | - Andrea Alegre-Martí
- Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona (UB), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
| | - Elise Gilson
- Laboratory of Gene Expression and Cancer, GIGA-Molecular & Computational Biology, University of Liège, 4000 Liège, Belgium
| | - Manan Krishnamurthy
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
| | - Li Wang
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, United States
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, United States
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Juan Fernández Recio
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
| | - Eva Estébanez-Perpiñá
- Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona (UB), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain
| | - Franck Dequiedt
- Laboratory of Gene Expression and Cancer, GIGA-Molecular & Computational Biology, University of Liège, 4000 Liège, Belgium
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
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Fettweis G, Wagh K, Stavreva DA, Jiménez-Panizo A, Kim S, Lion M, Alegre-Martí A, Rinaldi L, Johnson TA, Krishnamurthy M, Wang L, Ball DA, Karpova TS, Upadhyaya A, Vertommen D, Recio JF, Estébanez-Perpiñá E, Dequiedt F, Hager GL. Transcription factors form a ternary complex with NIPBL/MAU2 to localize cohesin at enhancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.12.09.627537. [PMID: 39713324 PMCID: PMC11661173 DOI: 10.1101/2024.12.09.627537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
While the cohesin complex is a key player in genome architecture, how it localizes to specific chromatin sites is not understood. Recently, we and others have proposed that direct interactions with transcription factors lead to the localization of the cohesin-loader complex (NIPBL/MAU2) within enhancers. Here, we identify two clusters of LxxLL motifs within the NIPBL sequence that regulate NIPBL dynamics, interactome, and NIPBL-dependent transcriptional programs. One of these clusters interacts with MAU2 and is necessary for the maintenance of the NIPBL-MAU2 heterodimer. The second cluster binds specifically to the ligand-binding domains of steroid receptors. For the glucocorticoid receptor (GR), we examine in detail its interaction surfaces with NIPBL and MAU2. Using AlphaFold2 and molecular docking algorithms, we uncover a GR-NIPBL-MAU2 ternary complex and describe its importance in GR-dependent gene regulation. Finally, we show that multiple transcription factors interact with NIPBL-MAU2, likely using interfaces other than those characterized for GR.
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Affiliation(s)
- Gregory Fettweis
- Laboratory of Gene Expression and Cancer, GIGA-Molecular & Computational Biology, University of Liège, 4000 Liège, Belgium
| | - Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diana A. Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alba Jiménez-Panizo
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michelle Lion
- Laboratory of Gene Expression and Cancer, GIGA-Molecular & Computational Biology, University of Liège, 4000 Liège, Belgium
| | - Andrea Alegre-Martí
- Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona (UB), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Present Address: Delfi Diagnostics Inc, Baltimore, MD 21224, USA
| | - Thomas A. Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Manan Krishnamurthy
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Present Address: Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Li Wang
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A. Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tatiana S. Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, Maryland 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Juan Fernández Recio
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - Eva Estébanez-Perpiñá
- Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona (UB), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain
| | - Franck Dequiedt
- Laboratory of Gene Expression and Cancer, GIGA-Molecular & Computational Biology, University of Liège, 4000 Liège, Belgium
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Lepagnol-Bestel AM, Haziza S, Viard J, Salin PA, Duchon A, Herault Y, Simonneau M. DYRK1A Up-Regulation Specifically Impairs a Presynaptic Form of Long-Term Potentiation. Life (Basel) 2025; 15:149. [PMID: 40003558 PMCID: PMC11856406 DOI: 10.3390/life15020149] [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: 12/22/2024] [Revised: 01/12/2025] [Accepted: 01/17/2025] [Indexed: 02/27/2025] Open
Abstract
Chromosome 21 DYRK1A kinase is associated with a variety of neuronal diseases including Down syndrome. However, the functional impact of this kinase at the synapse level remains unclear. We studied a mouse model that incorporated YAC 152F7 (570 kb), encoding six chromosome 21 genes including DYRK1A. The 152F7 mice displayed learning difficulties but their N-methyl-D-aspartate (NMDA)-dependent synaptic long-term potentiation is indistinguishable from non-transgenic animals. We have demonstrated that a presynaptic form of NMDA-independent long-term potentiation (LTP) at the hippocampal mossy fiber was impaired in the 152F7 animals. To obtain insights into the molecular mechanisms involved in such synaptic changes, we analyzed the Dyrk1a interactions with chromatin remodelers. We found that the number of DYRK1A-EP300 and DYRK1A-CREBPP increased in 152F7 mice. Moreover, we observed a transcriptional decrease in genes encoding presynaptic proteins involved in glutamate vesicle exocytosis, namely Rims1, Munc13-1, Syn2 and Rab3A.To refine our findings, we used a mouse BAC 189N3 (152 kb) line that only triplicates the gene Dyrk1a. Again, we found that this NMDA-independent form of LTP is impaired in this mouse line. Altogether, our results demonstrate that Dyrk1a up-regulation is sufficient to specifically inhibit the NMDA-independent form of LTP and suggest that this inhibition is linked to chromatin changes that deregulate genes encoding proteins involved in glutamate synaptic release.
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Affiliation(s)
| | - Simon Haziza
- Centre Psychiatrie & Neurosciences, INSERM U894, 75014 Paris, France; (A.-M.L.-B.); (S.H.); (J.V.)
- Centre National de la Recherche Scientifique, Université Paris-Saclay, CentraleSupélec, École Normale Supérieure Paris-Saclay, LuMIn, 91190 Gif-sur-Yvette, France
| | - Julia Viard
- Centre Psychiatrie & Neurosciences, INSERM U894, 75014 Paris, France; (A.-M.L.-B.); (S.H.); (J.V.)
| | - Paul A. Salin
- Centre de Recherche en Neuroscience de Lyon CRNL (INSERM U1028), Université Claude-Bernard Lyon 1, 69100 Lyon, France;
| | - Arnaud Duchon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM, U964, 67404 Illkirch, France; (A.D.); (Y.H.)
- Phenomin, Institut Clinique de la Souris (ICS), GIE CERBM, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM, U964, 67404 Illkirch, France; (A.D.); (Y.H.)
- Phenomin, Institut Clinique de la Souris (ICS), GIE CERBM, CNRS, INSERM, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Michel Simonneau
- Centre Psychiatrie & Neurosciences, INSERM U894, 75014 Paris, France; (A.-M.L.-B.); (S.H.); (J.V.)
- Centre National de la Recherche Scientifique, Université Paris-Saclay, CentraleSupélec, École Normale Supérieure Paris-Saclay, LuMIn, 91190 Gif-sur-Yvette, France
- Département d’Enseignement et de Recherche en Biologie, École Normale Supérieure Paris-Saclay, 91190 Gif-sur-Yvette, France
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Yavuz S, Abraham TE, Houtsmuller AB, van Royen ME. Phase Separation Mediated Sub-Nuclear Compartmentalization of Androgen Receptors. Cells 2024; 13:1693. [PMID: 39451211 PMCID: PMC11506798 DOI: 10.3390/cells13201693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 10/10/2024] [Accepted: 10/11/2024] [Indexed: 10/26/2024] Open
Abstract
The androgen receptor (AR), a member of the nuclear steroid hormone receptor family of transcription factors, plays a crucial role not only in the development of the male phenotype but also in the development and growth of prostate cancer. While AR structure and AR interactions with coregulators and chromatin have been studied in detail, improving our understanding of AR function in gene transcription regulation, the spatio-temporal organization and the role of microscopically discernible AR foci in the nucleus are still underexplored. This review delves into the molecular mechanisms underlying AR foci formation, focusing on liquid-liquid phase separation and its role in spatially organizing ARs and their binding partners within the nucleus at transcription sites, as well as the influence of 3D-genome organization on AR-mediated gene transcription.
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Affiliation(s)
- Selçuk Yavuz
- Department of Pathology, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.E.v.R.)
| | - Tsion E. Abraham
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (T.E.A.)
| | - Adriaan B. Houtsmuller
- Department of Pathology, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.E.v.R.)
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (T.E.A.)
| | - Martin E. van Royen
- Department of Pathology, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (S.Y.); (M.E.v.R.)
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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: 6] [Impact Index Per Article: 6.0] [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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6
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Rega C, Kozik Z, Yu L, Tsitsa I, Martin LA, Choudhary J. Exploring the Spatial Landscape of the Estrogen Receptor Proximal Proteome With Antibody-Based Proximity Labeling. Mol Cell Proteomics 2024; 23:100702. [PMID: 38122900 PMCID: PMC10831774 DOI: 10.1016/j.mcpro.2023.100702] [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: 06/30/2023] [Revised: 11/07/2023] [Accepted: 12/17/2023] [Indexed: 12/23/2023] Open
Abstract
Estrogen receptor α (ERα) drives the transcription of genes involved in breast cancer (BC) progression, relying on coregulatory protein recruitment for its transcriptional and biological activities. Mutation of ERα as well as aberrant recruitment of its regulatory proteins contribute to tumor adaptation and drug resistance. Therefore, understanding the dynamic changes in ERα protein interaction networks is crucial for elucidating drug resistance mechanisms in BC. Despite progress in studying ERα-associated proteins, capturing subcellular transient interactions remains challenging and, as a result, significant number of important interactions remain undiscovered. In this study, we employed biotinylation by antibody recognition (BAR), an innovative antibody-based proximity labeling (PL) approach, coupled with mass spectrometry to investigate the ERα proximal proteome and its changes associated with resistance to aromatase inhibition, a key therapy used in the treatment of ERα-positive BC. We show that BAR successfully detected most of the known ERα interactors and mainly identified nuclear proteins, using either an epitope tag or endogenous antibody to target ERα. We further describe the ERα proximal proteome rewiring associated with resistance applying BAR to a panel of isogenic cell lines modeling tumor adaptation in the clinic. Interestingly, we find that ERα associates with some of the canonical cofactors in resistant cells and several proximal proteome changes are due to increased expression of ERα. Resistant models also show decreased levels of estrogen-regulated genes. Sensitive and resistant cells harboring a mutation in the ERα (Y537C) revealed a similar proximal proteome. We provide an ERα proximal protein network covering several novel ERα-proximal partners. These include proteins involved in highly dynamic processes such as sumoylation and ubiquitination difficult to detect with traditional protein interaction approaches. Overall, we present BAR as an effective approach to investigate the ERα proximal proteome in a spatial context and demonstrate its application in different experimental conditions.
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Affiliation(s)
- Camilla Rega
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom.
| | - Zuzanna Kozik
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Ifigenia Tsitsa
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Lesley-Ann Martin
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
| | - Jyoti Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom.
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7
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Adamson B, Brittain N, Walker L, Duncan R, Luzzi S, Rescigno P, Smith G, McGill S, Burchmore RJ, Willmore E, Hickson I, Robson CN, Bogdan D, Jimenez-Vacas JM, Paschalis A, Welti J, Yuan W, McCracken SR, Heer R, Sharp A, de Bono JS, Gaughan L. The catalytic subunit of DNA-PK regulates transcription and splicing of AR in advanced prostate cancer. J Clin Invest 2023; 133:e169200. [PMID: 37751307 PMCID: PMC10645393 DOI: 10.1172/jci169200] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023] Open
Abstract
Aberrant androgen receptor (AR) signaling drives prostate cancer (PC), and it is a key therapeutic target. Although initially effective, the generation of alternatively spliced AR variants (AR-Vs) compromises efficacy of treatments. In contrast to full-length AR (AR-FL), AR-Vs constitutively activate androgenic signaling and are refractory to the current repertoire of AR-targeting therapies, which together drive disease progression. There is an unmet clinical need, therefore, to develop more durable PC therapies that can attenuate AR-V function. Exploiting the requirement of coregulatory proteins for AR-V function has the capacity to furnish tractable routes for attenuating persistent oncogenic AR signaling in advanced PC. DNA-PKcs regulates AR-FL transcriptional activity and is upregulated in both early and advanced PC. We hypothesized that DNA-PKcs is critical for AR-V function. Using a proximity biotinylation approach, we demonstrated that the DNA-PK holoenzyme is part of the AR-V7 interactome and is a key regulator of AR-V-mediated transcription and cell growth in models of advanced PC. Crucially, we provide evidence that DNA-PKcs controls global splicing and, via RBMX, regulates the maturation of AR-V and AR-FL transcripts. Ultimately, our data indicate that targeting DNA-PKcs attenuates AR-V signaling and provide evidence that DNA-PKcs blockade is an effective therapeutic option in advanced AR-V-positive patients with PC.
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Affiliation(s)
- Beth Adamson
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
| | - Nicholas Brittain
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
| | - Laura Walker
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
| | - Ruaridh Duncan
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
| | - Sara Luzzi
- Newcastle University Biosciences Institute, International Centre for Life, Newcastle Upon Tyne, United Kingdom
| | - Pasquale Rescigno
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
| | - Graham Smith
- Newcastle University Bioinformatics Support Unit, Medical School, Newcastle Upon Tyne, United Kingdom
| | - Suzanne McGill
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard J.S. Burchmore
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Elaine Willmore
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
| | - Ian Hickson
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
| | - Craig N. Robson
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
| | - Denisa Bogdan
- The Institute for Cancer Research, London, United Kingdom
| | | | - Alec Paschalis
- The Institute for Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jonathan Welti
- The Institute for Cancer Research, London, United Kingdom
| | - Wei Yuan
- The Institute for Cancer Research, London, United Kingdom
| | - Stuart R. McCracken
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
| | - Rakesh Heer
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
- Division of Surgery, Imperial College London, London, United Kingdom
| | - Adam Sharp
- The Institute for Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Johann S. de Bono
- The Institute for Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Luke Gaughan
- Newcastle University Centre for Cancer, Paul O’Gorman Building, Newcastle Upon Tyne, United Kingdom
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8
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Bianchi L, Damiani I, Castiglioni S, Carleo A, De Salvo R, Rossi C, Corsini A, Bellosta S. Smooth Muscle Cell Phenotypic Switch Induced by Traditional Cigarette Smoke Condensate: A Holistic Overview. Int J Mol Sci 2023; 24:ijms24076431. [PMID: 37047404 PMCID: PMC10094728 DOI: 10.3390/ijms24076431] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/19/2023] [Accepted: 03/25/2023] [Indexed: 04/01/2023] Open
Abstract
Cigarette smoke (CS) is a risk factor for inflammatory diseases, such as atherosclerosis. CS condensate (CSC) contains lipophilic components that may represent a systemic cardiac risk factor. To better understand CSC effects, we incubated mouse and human aortic smooth muscle cells (SMCs) with CSC. We evaluated specific markers for contractile [i.e., actin, aortic smooth muscle (ACTA2), calponin-1 (CNN1), the Kruppel-like factor 4 (KLF4), and myocardin (MYOCD) genes] and inflammatory [i.e., IL-1β, and IL-6, IL-8, and galectin-3 (LGALS-3) genes] phenotypes. CSC increased the expression of inflammatory markers and reduced the contractile ones in both cell types, with KLF4 modulating the SMC phenotypic switch. Next, we performed a mass spectrometry-based differential proteomic approach on human SMCs and could show 11 proteins were significantly affected by exposition to CSC (FC ≥ 2.7, p ≤ 0.05). These proteins are active in signaling pathways related to expression of pro-inflammatory cytokines and IFN, inflammasome assembly and activation, cytoskeleton regulation and SMC contraction, mitochondrial integrity and cellular response to oxidative stress, proteostasis control via ubiquitination, and cell proliferation and epithelial-to-mesenchymal transition. Through specific bioinformatics resources, we showed their tight functional correlation in a close interaction niche mainly orchestrated by the interferon-induced double-stranded RNA-activated protein kinase (alternative name: protein kinase RNA-activated; PKR) (EIF2AK2/PKR). Finally, by combining gene expression and protein abundance data we obtained a hybrid network showing reciprocal integration of the CSC-deregulated factors and indicating KLF4 and PKR as the most relevant factors.
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9
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Eickhoff N, Bergman AM, Zwart W. Homing in on a Moving Target: Androgen Receptor Cistromic Plasticity in Prostate Cancer. Endocrinology 2022; 163:6705578. [PMID: 36125208 DOI: 10.1210/endocr/bqac153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Indexed: 11/19/2022]
Abstract
The androgen receptor (AR) is the critical driver in prostate cancer and exerts its function mainly through transcriptional control. Recent advances in clinical studies and cell line models have illustrated that AR chromatin binding features are not static; rather they are highly variable yet reproducibly altered between clinical stages. Extensive genomic analyses of AR chromatin binding features in different disease stages have revealed a high degree of plasticity of AR chromatin interactions in clinical samples. Mechanistically, AR chromatin binding patterns are associated with specific somatic mutations on AR and other permutations, including mutations of AR-interacting proteins. Here we summarize the most recent studies on how the AR cistrome is dynamically altered in prostate cancer models and patient samples, and what implications this has for the identification of therapeutic targets to avoid the emergence of treatment resistance.
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Affiliation(s)
- Nils Eickhoff
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600MB Eindhoven, The Netherlands
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10
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Dahiya UR, Heemers HV. Analyzing the Androgen Receptor Interactome in Prostate Cancer: Implications for Therapeutic Intervention. Cells 2022; 11:936. [PMID: 35326387 PMCID: PMC8946651 DOI: 10.3390/cells11060936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022] Open
Abstract
The androgen receptor (AR) is a member of the ligand-activated nuclear receptor family of transcription factors. AR's transactivation activity is turned on by the binding of androgens, the male sex steroid hormones. AR is critical for the development and maintenance of the male phenotype but has been recognized to also play an important role in human diseases. Most notably, AR is a major driver of prostate cancer (CaP) progression, which remains the second leading cause of cancer deaths in American men. Androgen deprivation therapies (ADTs) that interfere with interactions between AR and its activating androgen ligands have been the mainstay for treatment of metastatic CaP. Although ADTs are effective and induce remissions, eventually they fail, while the growth of the majority of ADT-resistant CaPs remains under AR's control. Alternative approaches to inhibit AR activity and bypass resistance to ADT are being sought, such as preventing the interaction between AR and its cofactors and coregulators that is needed to execute AR-dependent transcription. For such strategies to be efficient, the 3D conformation of AR complexes needs to be well-understood and AR-regulator interaction sites resolved. Here, we review current insights into these 3D structures and the protein interaction sites in AR transcriptional complexes. We focus on methods and technological approaches used to identify AR interactors and discuss challenges and limitations that need to be overcome for efficient therapeutic AR complex disruption.
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Affiliation(s)
| | - Hannelore V. Heemers
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, NB-40, 9500 Euclid Avenue, Cleveland, OH 44195, USA;
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11
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Özturan D, Morova T, Lack NA. Androgen Receptor-Mediated Transcription in Prostate Cancer. Cells 2022; 11:898. [PMID: 35269520 PMCID: PMC8909478 DOI: 10.3390/cells11050898] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
Androgen receptor (AR)-mediated transcription is critical in almost all stages of prostate cancer (PCa) growth and differentiation. This process involves a complex interplay of coregulatory proteins, chromatin remodeling complexes, and other transcription factors that work with AR at cis-regulatory enhancer regions to induce the spatiotemporal transcription of target genes. This enhancer-driven mechanism is remarkably dynamic and undergoes significant alterations during PCa progression. In this review, we discuss the AR mechanism of action in PCa with a focus on how cis-regulatory elements modulate gene expression. We explore emerging evidence of genetic variants that can impact AR regulatory regions and alter gene transcription in PCa. Finally, we highlight several outstanding questions and discuss potential mechanisms of this critical transcription factor.
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Affiliation(s)
- Doğancan Özturan
- School of Medicine, Koç University, Istanbul 34450, Turkey;
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Tunç Morova
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
| | - Nathan A. Lack
- School of Medicine, Koç University, Istanbul 34450, Turkey;
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
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12
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Agbo L, Blanchet SA, Kougnassoukou Tchara PE, Fradet-Turcotte A, Lambert JP. Comprehensive Interactome Mapping of Nuclear Receptors Using Proximity Biotinylation. Methods Mol Biol 2022; 2456:223-240. [PMID: 35612745 DOI: 10.1007/978-1-0716-2124-0_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nuclear receptors, including hormone receptors, perform their cellular activities by modulating their protein-protein interactions. They engage with specific ligands and translocate to the nucleus, where they bind the DNA and activate extensive transcriptional programs. Therefore, gaining a comprehensive overview of the protein-protein interactions they establish requires methods that function effectively throughout the cell with fast dynamics and high reproducibility. Focusing on estrogen receptor alpha (ESR1), the founding member of the nuclear receptor family, this chapter describes a new lentiviral system that allows the expression of TurboID-hemagglutinin (HA)-2 × Strep tagged proteins in mammalian cells to perform fast proximity biotinylation assays. Key validation steps for these reagents and their use in interactome mapping experiments in two distinct breast cancer cell lines are described. Our protocol enabled the quantification of ESR1 interactome generated by cellular contexts that were hormone-sensitive or not.
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Affiliation(s)
- Lynda Agbo
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Québec, QC, Canada
- Endocrinology and Nephrology Division, CHU de Québec-Université Laval Research Center, Québec, QC, Canada
| | - Sophie Anne Blanchet
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Pata-Eting Kougnassoukou Tchara
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Québec, QC, Canada
- Endocrinology and Nephrology Division, CHU de Québec-Université Laval Research Center, Québec, QC, Canada
| | - Amélie Fradet-Turcotte
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC, Canada.
- Department of Molecular Biology, Medical Biochemistry and Pathology, Cancer Research Center, Université Laval, Québec, QC, Canada.
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Québec, QC, Canada.
- Endocrinology and Nephrology Division, CHU de Québec-Université Laval Research Center, Québec, QC, Canada.
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13
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Proteomic Landscape of Prostate Cancer: The View Provided by Quantitative Proteomics, Integrative Analyses, and Protein Interactomes. Cancers (Basel) 2021; 13:cancers13194829. [PMID: 34638309 PMCID: PMC8507874 DOI: 10.3390/cancers13194829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer is the second most frequent cancer of men worldwide. While the genetic landscapes and heterogeneity of prostate cancer are relatively well-known already, methodological developments now allow for studying basic and dynamic proteomes on a large scale and in a quantitative fashion. This aids in revealing the functional output of cancer genomes. It has become evident that not all aberrations at the genetic and transcriptional level are translated to the proteome. In addition, the proteomic level contains heterogeneity, which increases as the cancer progresses from primary prostate cancer (PCa) to metastatic and castration-resistant prostate cancer (CRPC). While multiple aspects of prostate adenocarcinoma proteomes have been studied, less is known about proteomes of neuroendocrine prostate cancer (NEPC). In this review, we summarize recent developments in prostate cancer proteomics, concentrating on the proteomic landscapes of clinical prostate cancer, cell line and mouse model proteomes interrogating prostate cancer-relevant signaling and alterations, and key prostate cancer regulator interactomes, such as those of the androgen receptor (AR). Compared to genomic and transcriptomic analyses, the view provided by proteomics brings forward changes in prostate cancer metabolism, post-transcriptional RNA regulation, and post-translational protein regulatory pathways, requiring the full attention of studies in the future.
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