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Inoue T, Bao X, Kageyama T, Sugino Y, Sekito S, Miyachi S, Sasaki T, Getzenberg R. Purine-Rich Element Binding Protein Alpha, a Nuclear Matrix Protein, Has a Role in Prostate Cancer Progression. Int J Mol Sci 2024; 25:6911. [PMID: 39000020 PMCID: PMC11241608 DOI: 10.3390/ijms25136911] [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: 05/22/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Solid tumors as well as leukemias and lymphomas show striking changes in nuclear structure including nuclear size and shape, the number and size of nucleoli, and chromatin texture. These alterations have been used in cancer diagnosis and might be related to the altered functional properties of cancer cells. The nuclear matrix (NM) represents the structural composition of the nucleus and consists of nuclear lamins and pore complexes, an internal ribonucleic protein network, and residual nucleoli. In the nuclear microenvironment, the NM is associated with multi-protein complexes, such as basal transcription factors, signaling proteins, histone-modifying factors, and chromatin remodeling machinery directly or indirectly through scaffolding proteins. Therefore, alterations in the composition of NM could result in altered DNA topology and changes in the interaction of various genes, which could then participate in a cascade of the cancer process. Using an androgen-sensitive prostate cancer cell line, LNCaP, and its androgen-independent derivative, LN96, conventional 2D-proteomic analysis of the NM proteins revealed that purine-rich element binding protein alpha (PURα) was detected in the NM proteins and differentially expressed between the cell lines. In this article, we will review the potential role of the molecule in prostate cancer.
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Affiliation(s)
- Takahiro Inoue
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu 514-0001, Japan; (X.B.); (T.K.); (Y.S.); (S.S.); (S.M.); (T.S.)
| | - Xin Bao
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu 514-0001, Japan; (X.B.); (T.K.); (Y.S.); (S.S.); (S.M.); (T.S.)
| | - Takumi Kageyama
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu 514-0001, Japan; (X.B.); (T.K.); (Y.S.); (S.S.); (S.M.); (T.S.)
| | - Yusuke Sugino
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu 514-0001, Japan; (X.B.); (T.K.); (Y.S.); (S.S.); (S.M.); (T.S.)
| | - Sho Sekito
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu 514-0001, Japan; (X.B.); (T.K.); (Y.S.); (S.S.); (S.M.); (T.S.)
| | - Shiori Miyachi
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu 514-0001, Japan; (X.B.); (T.K.); (Y.S.); (S.S.); (S.M.); (T.S.)
| | - Takeshi Sasaki
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu 514-0001, Japan; (X.B.); (T.K.); (Y.S.); (S.S.); (S.M.); (T.S.)
| | - Robert Getzenberg
- Dr. Kiran C Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA;
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Swaminathan G, Rogel-Ayala DG, Armich A, Barreto G. Implications in Cancer of Nuclear Micro RNAs, Long Non-Coding RNAs, and Circular RNAs Bound by PRC2 and FUS. Cancers (Basel) 2024; 16:868. [PMID: 38473229 DOI: 10.3390/cancers16050868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The eukaryotic genome is mainly transcribed into non-coding RNAs (ncRNAs), including different RNA biotypes, such as micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), among others. Although miRNAs are assumed to act primarily in the cytosol, mature miRNAs have been reported and functionally characterized in the nuclei of different cells. Further, lncRNAs are important regulators of different biological processes in the cell nucleus as part of different ribonucleoprotein complexes. CircRNAs constitute a relatively less-characterized RNA biotype that has a circular structure as result of a back-splicing process. However, circRNAs have recently attracted attention in different scientific fields due to their involvement in various biological processes and pathologies. In this review, we will summarize recent studies that link to cancer miRNAs that have been functionally characterized in the cell nucleus, as well as lncRNAs and circRNAs that are bound by core components of the polycomb repressive complex 2 (PRC2) or the protein fused in sarcoma (FUS), highlighting mechanistic aspects and their diagnostic and therapeutic potential.
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Affiliation(s)
| | - Diana G Rogel-Ayala
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Amine Armich
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, F-54000 Nancy, France
| | - Guillermo Barreto
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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Wang X, Liu J, Mao C, Mao Y. Phase separation-mediated biomolecular condensates and their relationship to tumor. Cell Commun Signal 2024; 22:143. [PMID: 38383403 PMCID: PMC10880379 DOI: 10.1186/s12964-024-01518-9] [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: 09/29/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Phase separation is a cellular phenomenon where macromolecules aggregate or segregate, giving rise to biomolecular condensates resembling "droplets" and forming distinct, membrane-free compartments. This process is pervasive in biological cells, contributing to various essential cellular functions. However, when phase separation goes awry, leading to abnormal molecular aggregation, it can become a driving factor in the development of diseases, including tumor. Recent investigations have unveiled the intricate connection between dysregulated phase separation and tumor pathogenesis, highlighting its potential as a novel therapeutic target. This article provides an overview of recent phase separation research, with a particular emphasis on its role in tumor, its therapeutic implications, and outlines avenues for further exploration in this intriguing field.
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Affiliation(s)
- Xi Wang
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Jiameng Liu
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Chaoming Mao
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
| | - Yufei Mao
- Department of Ultrasound Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
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Rubio K, Hernández-Cruz EY, Rogel-Ayala DG, Sarvari P, Isidoro C, Barreto G, Pedraza-Chaverri J. Nutriepigenomics in Environmental-Associated Oxidative Stress. Antioxidants (Basel) 2023; 12:771. [PMID: 36979019 PMCID: PMC10045733 DOI: 10.3390/antiox12030771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Complex molecular mechanisms define our responses to environmental stimuli. Beyond the DNA sequence itself, epigenetic machinery orchestrates changes in gene expression induced by diet, physical activity, stress and pollution, among others. Importantly, nutrition has a strong impact on epigenetic players and, consequently, sustains a promising role in the regulation of cellular responses such as oxidative stress. As oxidative stress is a natural physiological process where the presence of reactive oxygen-derived species and nitrogen-derived species overcomes the uptake strategy of antioxidant defenses, it plays an essential role in epigenetic changes induced by environmental pollutants and culminates in signaling the disruption of redox control. In this review, we present an update on epigenetic mechanisms induced by environmental factors that lead to oxidative stress and potentially to pathogenesis and disease progression in humans. In addition, we introduce the microenvironment factors (physical contacts, nutrients, extracellular vesicle-mediated communication) that influence the epigenetic regulation of cellular responses. Understanding the mechanisms by which nutrients influence the epigenome, and thus global transcription, is crucial for future early diagnostic and therapeutic efforts in the field of environmental medicine.
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Affiliation(s)
- Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Estefani Y. Hernández-Cruz
- Postgraduate in Biological Sciences, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
| | - Diana G. Rogel-Ayala
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | | | - Ciro Isidoro
- Department of Health Sciences, Università del Piemonte Orientale, Via Paolo Solaroli 17, 28100 Novara, Italy
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
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Wang J, Meng F, Mao F. Single cell sequencing analysis and transcriptome analysis constructed the liquid-liquid phase separation(LLPS)-related prognostic model for endometrial cancer. Front Oncol 2022; 12:1005472. [PMID: 36185238 PMCID: PMC9515536 DOI: 10.3389/fonc.2022.1005472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background Endometrial cancer is one of the most common gynecological tumors in developed countries. Our understanding of the pathogenesis of endometrial cancer and the changes in the immune microenvironment are still unclear. It is necessary to explore new biomarkers to guide the diagnosis and treatment of endometrial cancer. Methods The GEO database was used to download the endometrial cancer single cell sequencing dataset GSE173682. The UCSC database was used to download transcriptome sequencing data. The validation set was the transcriptome dataset GSE119041, which was retrieved from the GEO database. On the DrLLPS website, liquid-liquid phase separation-related genes can be downloaded. Relevant hub genes were found using weighted co-expression network analysis and dimension reduction clustering analysis. Prognostic models were built using Lasso regression and univariate COX regression. Analyses of immune infiltration were employed to investigate the endometrial cancer immunological microenvironment. The expression of model genes in endometrial cancer was confirmed using a PCR test. Results We created an LLPS-related predictive model for endometrial cancer by extensive study, and it consists of four genes: EIF2S2, SNRPC, PRELID1, and NDUFB9. Patients with endometrial cancer may be classified into high-risk and low-risk groups based on their risk scores, and those in the high-risk group had significantly worse prognoses (P<0.05). Additionally, there were notable variations in the immunological milieu between the groups at high and low risk. EIF2S2, SNRPC, PRELID1, and NDUFB9 were all up-regulated in endometrial cancer tissues, according to PCR results. Conclusions Our study can provide a certain reference for the diagnosis and treatment of endometrial cancer.
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Affiliation(s)
- Jiayang Wang
- Department of Radiotherapy, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
| | - Fei Meng
- Department of Gynaecology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
| | - Fei Mao
- Department of Urology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
- *Correspondence: Fei Mao,
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Vieujean S, Caron B, Haghnejad V, Jouzeau JY, Netter P, Heba AC, Ndiaye NC, Moulin D, Barreto G, Danese S, Peyrin-Biroulet L. Impact of the Exposome on the Epigenome in Inflammatory Bowel Disease Patients and Animal Models. Int J Mol Sci 2022; 23:7611. [PMID: 35886959 PMCID: PMC9321337 DOI: 10.3390/ijms23147611] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic inflammatory disorders of the gastrointestinal tract that encompass two main phenotypes, namely Crohn's disease and ulcerative colitis. These conditions occur in genetically predisposed individuals in response to environmental factors. Epigenetics, acting by DNA methylation, post-translational histones modifications or by non-coding RNAs, could explain how the exposome (or all environmental influences over the life course, from conception to death) could influence the gene expression to contribute to intestinal inflammation. We performed a scoping search using Medline to identify all the elements of the exposome that may play a role in intestinal inflammation through epigenetic modifications, as well as the underlying mechanisms. The environmental factors epigenetically influencing the occurrence of intestinal inflammation are the maternal lifestyle (mainly diet, the occurrence of infection during pregnancy and smoking); breastfeeding; microbiota; diet (including a low-fiber diet, high-fat diet and deficiency in micronutrients); smoking habits, vitamin D and drugs (e.g., IBD treatments, antibiotics and probiotics). Influenced by both microbiota and diet, short-chain fatty acids are gut microbiota-derived metabolites resulting from the anaerobic fermentation of non-digestible dietary fibers, playing an epigenetically mediated role in the integrity of the epithelial barrier and in the defense against invading microorganisms. Although the impact of some environmental factors has been identified, the exposome-induced epimutations in IBD remain a largely underexplored field. How these environmental exposures induce epigenetic modifications (in terms of duration, frequency and the timing at which they occur) and how other environmental factors associated with IBD modulate epigenetics deserve to be further investigated.
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Affiliation(s)
- Sophie Vieujean
- Hepato-Gastroenterology and Digestive Oncology, University Hospital CHU of Liège, 4000 Liege, Belgium;
| | - Bénédicte Caron
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Vincent Haghnejad
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Jean-Yves Jouzeau
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Patrick Netter
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Anne-Charlotte Heba
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - Ndeye Coumba Ndiaye
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - David Moulin
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Guillermo Barreto
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Universidad de la Salud del Estado de Puebla, Puebla 72000, Mexico
| | - Silvio Danese
- Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and University Vita-Salute San Raffaele, 20132 Milan, Italy;
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
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Therapeutics-how to treat phase separation-associated diseases. Emerg Top Life Sci 2021; 4:307-318. [PMID: 32364240 PMCID: PMC7733670 DOI: 10.1042/etls20190176] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022]
Abstract
Liquid-liquid phase separation has drawn attention as many neurodegeneration or cancer-associated proteins are able to form liquid membraneless compartments (condensates) by liquid-liquid phase separation. Furthermore, there is rapidly growing evidence that disease-associated mutation or post-translational modification of these proteins causes aberrant location, composition or physical properties of the condensates. It is ambiguous whether aberrant condensates are always causative in disease mechanisms, however they are likely promising potential targets for therapeutics. The conceptual framework of liquid-liquid phase separation provides opportunities for novel therapeutic approaches. This review summarises how the extensive recent advances in understanding control of nucleation, growth and composition of condensates by protein post-translational modification has revealed many possibilities for intervention by conventional small molecule enzyme inhibitors. This includes the first proof-of-concept examples. However, understanding membraneless organelle formation as a physical chemistry process also highlights possible physicochemical mechanisms of intervention. There is huge demand for innovation in drug development, especially for challenging diseases of old age including neurodegeneration and cancer. The conceptual framework of liquid-liquid phase separation provides a new paradigm for thinking about modulating protein function and is very different from enzyme lock-and-key or structured binding site concepts and presents new opportunities for innovation.
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Arun G, Aggarwal D, Spector DL. MALAT1 Long Non-Coding RNA: Functional Implications. Noncoding RNA 2020; 6:E22. [PMID: 32503170 PMCID: PMC7344863 DOI: 10.3390/ncrna6020022] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022] Open
Abstract
The mammalian genome is pervasively transcribed and the functional significance of many long non-coding RNA (lncRNA) transcripts are gradually being elucidated. Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is one of the most well-studied lncRNAs. MALAT1 is a highly conserved nuclear retained lncRNA that is abundantly expressed in cells and tissues and has been shown to play a role in regulating genes at both the transcriptional and post-transcriptional levels in a context-dependent manner. However, Malat1 has been shown to be dispensable for normal development and viability in mice. Interestingly, accumulating evidence suggests that MALAT1 plays an important role in numerous diseases including cancer. Here, we discuss the current state-of-knowledge in regard to MALAT1 with respect to its function, role in diseases, and the potential therapeutic opportunities for targeting MALAT1 using antisense oligonucleotides and small molecules.
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Affiliation(s)
- Gayatri Arun
- Envisagenics, 101 Avenue of the Americas, New York, NY 10013, USA;
| | - Disha Aggarwal
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, NY 11794, USA;
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
| | - David L. Spector
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, NY 11794, USA;
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
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Rubio K, Castillo-Negrete R, Barreto G. Non-coding RNAs and nuclear architecture during epithelial-mesenchymal transition in lung cancer and idiopathic pulmonary fibrosis. Cell Signal 2020; 70:109593. [PMID: 32135188 DOI: 10.1016/j.cellsig.2020.109593] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/13/2022]
Abstract
Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. On the other hand, idiopathic pulmonary fibrosis (IPF) is the most common interstitial lung disease showing a prevalence of 20 new cases per 100,000 persons per year. Despite differences in cellular origin and pathological phenotypes, LC and IPF are lung diseases that share common features, including hyperproliferation of specific cell types in the lung, involvement of epithelial-mesenchymal transition (EMT) and enhanced activity of signaling pathways, such as tissue growth factor (TGFB), epidermal growth factor (EGF), fibroblast growth factor (FGF), wingless secreted glycoprotein (WNT) signaling, among others. EMT is a process during which epithelial cells lose their cell polarity and cell-cell adhesion, and acquire migratory and invasive properties to become mesenchymal cells. EMT involves numerous morphological hallmarks of hyperproliferative diseases, like cell plasticity, resistance to apoptosis, dedifferentiation and proliferation, thereby playing a central role during organ fibrosis and cancer progression. EMT was considered as an "all-or-none" process. In contrast to these outdated dichotomist interpretations, recent reports suggest that EMT occurs gradually involving different epithelial cell intermediate states with mesenchyme-like characteristics. These cell intermediate states of EMT differ from each other in their cell plasticity, invasiveness and metastatic potential, which in turn are induced by signals from their microenvironment. EMT is regulated by several transcription factors (TFs), which are members of prominent families of master regulators of transcription. In addition, there is increasing evidence for the important contribution of noncoding RNAs (ncRNAs) to EMT. In our review we highlight articles dissecting the function of different ncRNAs subtypes and nuclear architecture in cell intermediate states of EMT, as well as their involvement in LC and IPF.
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Affiliation(s)
- Karla Rubio
- Brain and Lung Epigenetics (BLUE), Glycobiology, Cell Growth and Tissue Repair Research Unit (Gly-CRRET), Université Paris-Est Créteil (UPEC), 94010 Créteil, France; Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstraße 1, 61231 Bad Nauheim, Germany
| | - Rafael Castillo-Negrete
- Brain and Lung Epigenetics (BLUE), Glycobiology, Cell Growth and Tissue Repair Research Unit (Gly-CRRET), Université Paris-Est Créteil (UPEC), 94010 Créteil, France; Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstraße 1, 61231 Bad Nauheim, Germany
| | - Guillermo Barreto
- Brain and Lung Epigenetics (BLUE), Glycobiology, Cell Growth and Tissue Repair Research Unit (Gly-CRRET), Université Paris-Est Créteil (UPEC), 94010 Créteil, France; Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstraße 1, 61231 Bad Nauheim, Germany; Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russian Federation; Universities of Giessen and Marburg Lung Center (UGMLC), The German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Germany.
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10
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p53 CRISPR Deletion Affects DNA Structure and Nuclear Architecture. J Clin Med 2020; 9:jcm9020598. [PMID: 32098416 PMCID: PMC7073688 DOI: 10.3390/jcm9020598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 01/10/2023] Open
Abstract
The TP53 gene is a key tumor suppressor. Although the tumor suppressor p53 was one of the first to be characterized as a transcription factor, with its main function potentiated by its interaction with DNA, there are still many unresolved questions about its mechanism of action. Here, we demonstrate a novel role for p53 in the maintenance of nuclear architecture of cells. Using three-dimensional (3D) imaging and spectral karyotyping, as well as super resolution microscopy of DNA structure, we observe significant differences in 3D telomere signatures, DNA structure and DNA-poor spaces as well gains or losses of chromosomes, between normal and tumor cells with CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-deleted or wild-type TP53. Additionally, treatment with Nutlin-3 results in differences in nuclear architecture of telomeres in wild-type but not in p53 knockout MCF-7 (Michigan Cancer Foundation-7) cells. Nutlin-3 binds to the p53-binding pocket of mouse double minute 2 (MDM2) and blocks the p53-MDM2 interaction. Moreover, we demonstrate that another p53 stabilizing small molecule, RITA (reactivation of p53 and induction of tumor cell apoptosis), also induces changes in 3D DNA structure, apparently in a p53 independent manner. These results implicate p53 activity in regulating nuclear organization and, additionally, highlight the divergent effects of the p53 targeting compounds Nutlin-3 and RITA.
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11
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Rubio K, Singh I, Dobersch S, Sarvari P, Günther S, Cordero J, Mehta A, Wujak L, Cabrera-Fuentes H, Chao CM, Braubach P, Bellusci S, Seeger W, Günther A, Preissner KT, Wygrecka M, Savai R, Papy-Garcia D, Dobreva G, Heikenwalder M, Savai-Pullamsetti S, Braun T, Barreto G. Inactivation of nuclear histone deacetylases by EP300 disrupts the MiCEE complex in idiopathic pulmonary fibrosis. Nat Commun 2019; 10:2229. [PMID: 31110176 PMCID: PMC6527704 DOI: 10.1038/s41467-019-10066-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 04/12/2019] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and highly lethal lung disease with unknown etiology and poor prognosis. IPF patients die within 2 years after diagnosis mostly due to respiratory failure. Current treatments against IPF aim to ameliorate patient symptoms and to delay disease progression. Unfortunately, therapies targeting the causes of or reverting IPF have not yet been developed. Here we show that reduced levels of miRNA lethal 7d (MIRLET7D) in IPF compromise epigenetic gene silencing mediated by the ribonucleoprotein complex MiCEE. In addition, we find that hyperactive EP300 reduces nuclear HDAC activity and interferes with MiCEE function in IPF. Remarkably, EP300 inhibition reduces fibrotic hallmarks of in vitro (patient-derived primary fibroblast), in vivo (bleomycin mouse model), and ex vivo (precision-cut lung slices, PCLS) IPF models. Our work provides the molecular basis for therapies against IPF using EP300 inhibition. Idiopathic pulmonary fibrosis (IPF) is a lethal disease with insufficient treatment strategies. Here the authors show that reduction of the microRNA MIRLET7D and hyperactivation of EP300 contribute to impaired epigenetic silencing by the MiCEE complex in pulmonary fibroblasts of IPF patients, and demonstrate the benefit of inhibiting EP300 for the treatment of IPF.
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Affiliation(s)
- Karla Rubio
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Indrabahadur Singh
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany. .,Division Chronic Inflammation and Cancer (F180), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
| | - Stephanie Dobersch
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Pouya Sarvari
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Stefan Günther
- Department of Cardiac Development, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
| | - Julio Cordero
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Anatomy and Developmental Biology, CBTM, Heidelberg University, Mannheim, 68167, Germany.,European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany
| | - Aditi Mehta
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Pharmaceutical Technology and Biopharmaceutics, Department of Pharmacy, Ludwig-Maximilians-University of Munich, Munich, 81377, Germany
| | - Lukasz Wujak
- Faculty of Medicine, Biochemistry Institute, Justus Liebig University, Giessen, 35392, Germany
| | - Hector Cabrera-Fuentes
- Faculty of Medicine, Biochemistry Institute, Justus Liebig University, Giessen, 35392, Germany.,National Heart Research Institute, National Heart Centre Singapore, Singapore, 169609, Singapore.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russian Federation.,Tecnologico de Monterrey, Centro de Biotecnologia-FEMSA, Monterrey, 64849, NL, Mexico.,Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, 169609, Singapore
| | - Cho-Ming Chao
- Chair for Lung Matrix Remodeling, Excellence Cluster Cardio Pulmonary System, Justus Liebig University, Giessen, 35392, Germany.,International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University and Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang, 325035, China.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany.,Department of General Pediatrics and Neonatology, University Children's Hospital Giessen, Justus Liebig University, Giessen, 35392, Germany
| | - Peter Braubach
- German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany.,Institute for Pathology, Hanover Medical School, Hanover, 30625, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hanover (BREATH) Research Network, Hanover, 30625, Germany
| | - Saverio Bellusci
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russian Federation.,Chair for Lung Matrix Remodeling, Excellence Cluster Cardio Pulmonary System, Justus Liebig University, Giessen, 35392, Germany.,International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University and Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang, 325035, China.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany
| | - Werner Seeger
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,Department of General Pediatrics and Neonatology, University Children's Hospital Giessen, Justus Liebig University, Giessen, 35392, Germany.,Pulmonary and Critical Care Medicine, Department of Internal Medicine, Justus Liebig University, Giessen, 35392, Germany
| | - Andreas Günther
- Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany.,Pulmonary and Critical Care Medicine, Department of Internal Medicine, Justus Liebig University, Giessen, 35392, Germany.,Agaplesion Lung Clinic Waldhof Elgershausen, Greifenstein, 35753, Germany
| | - Klaus T Preissner
- Faculty of Medicine, Biochemistry Institute, Justus Liebig University, Giessen, 35392, Germany.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russian Federation.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany
| | - Malgorzata Wygrecka
- Faculty of Medicine, Biochemistry Institute, Justus Liebig University, Giessen, 35392, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany
| | - Rajkumar Savai
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany
| | - Dulce Papy-Garcia
- Laboratoire Croissance, Réparation et Régénération Tissulaires (CRRET), CNRS ERL 9215, Université Paris Est Créteil, Université Paris Est, Créteil, F-94000, France
| | - Gergana Dobreva
- Anatomy and Developmental Biology, CBTM, Heidelberg University, Mannheim, 68167, Germany.,European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany
| | - Mathias Heikenwalder
- Division Chronic Inflammation and Cancer (F180), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Soni Savai-Pullamsetti
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany.,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany
| | - Thomas Braun
- Department of Cardiac Development, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany.,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany
| | - Guillermo Barreto
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany. .,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russian Federation. .,Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), The Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, 35392, Germany. .,German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), UGMLC, Giessen, 35392, Germany. .,Laboratoire Croissance, Réparation et Régénération Tissulaires (CRRET), CNRS ERL 9215, Université Paris Est Créteil, Université Paris Est, Créteil, F-94000, France.
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12
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Dobersch S, Rubio K, Barreto G. Pioneer Factors and Architectural Proteins Mediating Embryonic Expression Signatures in Cancer. Trends Mol Med 2019; 25:287-302. [PMID: 30795971 DOI: 10.1016/j.molmed.2019.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/18/2022]
Abstract
Accumulation of mutations causing aberrant changes in the genome promotes cancer. However, mutations do not occur in every cancer subtype, suggesting additional events that trigger cancer. Chromatin rearrangements initiated by pioneer factors and architectural proteins are key events occurring before cancer-related genes are expressed. Both protein groups are also master regulators of important processes during embryogenesis. Several publications demonstrated that embryonic gene expression signatures are reactivated during cancer. This review article highlights current knowledge on pioneer factors and architectural proteins mediating chromatin rearrangements, which are the backbone of embryonic expression signatures promoting malignant transformation. Understanding chromatin rearrangements inducing embryonic expression signatures in adult cells might be the key to novel therapeutic approaches against cancers subtypes that arise without genomic mutations.
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Affiliation(s)
- Stephanie Dobersch
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Karla Rubio
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Guillermo Barreto
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany; Laboratoire Croissance, Réparation et Régénération Tissulaires (CRRET), CNRS ERL 9215, Université Paris Est Créteil, Université Paris Est, F-94000, Créteil, France; Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russian Federation; Member of the Excellence Cluster Cardio Pulmonary System (ECCPS), Universities of Giessen and Marburg Lung Center (UGMLC), 35932 Giessen, Germany; Member of the German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL).
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