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Cubiella T, Celada L, San-Juan-Guardado J, Rodríguez-Aguilar R, Suárez-Priede Á, Poch M, Dominguez F, Fernández-Vega I, Montero-Pavón P, Fraga MF, Nakatani Y, Takata S, Yachida S, Valdés N, Chiara MD. PCDHGC3 hypermethylation as a potential biomarker of intestinal neuroendocrine carcinomas. J Pathol 2024; 263:418-428. [PMID: 38795318 DOI: 10.1002/path.6291] [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: 10/31/2023] [Revised: 02/09/2024] [Accepted: 04/03/2024] [Indexed: 05/27/2024]
Abstract
Neuroendocrine neoplasms (NENs) encompass tumors arising from neuroendocrine cells in various organs, including the gastrointestinal tract, pancreas, adrenal gland, and paraganglia. Despite advancements, accurately predicting the aggressiveness of gastroenteropancreatic (GEP) NENs based solely on pathological data remains challenging, thereby limiting optimal clinical management. Our previous research unveiled a crucial link between hypermethylation of the protocadherin PCDHGC3 gene and neuroendocrine tumors originating from the paraganglia and adrenal medulla. This epigenetic alteration was associated with increased metastatic potential and succinate dehydrogenase complex (SDH) dysfunction. Expanding upon this discovery, the current study explored PCDHGC3 gene methylation within the context of GEP-NENs in a cohort comprising 34 cases. We uncovered promoter hypermethylation of PCDHGC3 in 29% of GEP-NENs, with a significantly higher prevalence in gastrointestinal (GI) neuroendocrine carcinomas (NECs) compared with both pancreatic (Pan) NECs and neuroendocrine tumors (NETs) of GI and Pan origin. Importantly, these findings were validated in one of the largest multi-center GEP-NEN cohorts. Mechanistic analysis revealed that PCDHGC3 hypermethylation was not associated with SDH mutations or protein loss, indicating an SDH-independent epigenetic mechanism. Clinically, PCDHGC3 hypermethylation emerged as a significant prognostic factor, correlating with reduced overall survival rates in both patient cohorts. Significantly, whereas PCDHGC3 hypermethylation exhibited a strong correlation with TP53 somatic mutations, a hallmark of NEC, its predictive value surpassed that of TP53 mutations, with an area under the curve (AUC) of 0.95 (95% CI 0.83-1.0) for discriminating GI-NECs from GI-NETs, highlighting its superior predictive performance. In conclusion, our findings position PCDHGC3 methylation status as a promising molecular biomarker for effectively stratifying patients with GI-NENs. This discovery has the potential to advance patient care by enabling more precise risk assessments and tailored treatment strategies. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Tamara Cubiella
- Health Research Institute of the Principado de Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of the Principado de Asturias, University of Oviedo, Oviedo, Spain
| | - Lucía Celada
- Health Research Institute of the Principado de Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of the Principado de Asturias, University of Oviedo, Oviedo, Spain
| | - Jaime San-Juan-Guardado
- Health Research Institute of the Principado de Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of the Principado de Asturias, University of Oviedo, Oviedo, Spain
| | | | - Álvaro Suárez-Priede
- Health Research Institute of the Principado de Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of the Principado de Asturias, University of Oviedo, Oviedo, Spain
| | - María Poch
- Department of Pathology, Hospital Universitario de Cabueñes, Gijón, Spain
| | | | - Iván Fernández-Vega
- Department of Pathology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Pedro Montero-Pavón
- Department of Pathology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Mario F Fraga
- Health Research Institute of the Principado de Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of the Principado de Asturias, University of Oviedo, Oviedo, Spain
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), El Entrego, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), Madrid, Spain
| | - Yoichiro Nakatani
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Japan
| | - So Takata
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Nuria Valdés
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), Madrid, Spain
- Hospital Universitario Cruces, Bizkaia, Spain
- Biobizkaia Health Research Institute, Bizkaia, Spain
- CIBERDEM (Network of Biomedical Research in Diabetes), Madrid, Spain
| | - María-Dolores Chiara
- Health Research Institute of the Principado de Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of the Principado de Asturias, University of Oviedo, Oviedo, Spain
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2
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Long RM, Ong H, Wang WX, Komirishetty P, Areti A, Chandrasekhar A, Larouche M, Lefebvre JL, Zochodne DW. The Role of Protocadherin γ in Adult Sensory Neurons and Skin Reinnervation. J Neurosci 2023; 43:8348-8366. [PMID: 37821230 PMCID: PMC10711737 DOI: 10.1523/jneurosci.1940-22.2023] [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: 10/14/2022] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023] Open
Abstract
The clustered protocadherins (cPcdhs) play a critical role in the patterning of several CNS axon and dendritic arbors, through regulation of homophilic self and neighboring interactions. While not explored, primary peripheral sensory afferents that innervate the epidermis may require similar constraints to convey spatial signals with appropriate fidelity. Here, we show that members of the γ-Pcdh (Pcdhγ) family are expressed in both adult sensory neuron axons and in neighboring keratinocytes that have close interactions during skin reinnervation. Adult mice of both sexes were studied. Pcdhγ knock-down either through small interfering RNA (siRNA) transduction or AAV-Cre recombinase transfection of adult mouse primary sensory neurons from floxed Pcdhγ mice was associated with a remarkable rise in neurite outgrowth and branching. Rises in outgrowth were abrogated by Rac1 inhibition. Moreover, AAV-Cre knock-down in Pcdhγ floxed neurons generated a rise in neurite self-intersections, and a robust rise in neighbor intersections or tiling, suggesting a role in sensory axon repulsion. Interestingly, preconditioned (3-d axotomy) neurons with enhanced growth had temporary declines in Pcdhγ and lessened outgrowth from Pcdhγ siRNA. In vivo, mice with local hindpaw skin Pcdhγ knock-down by siRNA had accelerated reinnervation by new epidermal axons with greater terminal branching and reduced intra-axonal spacing. Pcdhγ knock-down also had reciprocal impacts on keratinocyte density and nuclear size. Taken together, this work provides evidence for a role of Pcdhγ in attenuating outgrowth of sensory axons and their interactions, with implications in how new reinnervating axons following injury fare amid skin keratinocytes that also express Pcdhγ.SIGNIFICANCE STATEMENT The molecular mechanisms and potential constraints that govern skin reinnervation and patterning by sensory axons are largely unexplored. Here, we show that γ-protocadherins (Pcdhγ) may help to dictate interaction not only among axons but also between axons and keratinocytes as the former re-enter the skin during reinnervation. Pcdhγ neuronal knock-down enhances outgrowth in peripheral sensory neurons, involving the growth cone protein Rac1 whereas skin Pcdhγ knock-down generates rises in terminal epidermal axon growth and branching during re-innervation. Manipulation of sensory axon regrowth within the epidermis offers an opportunity to influence regenerative outcomes following nerve injury.
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Affiliation(s)
- Rebecca M Long
- Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Honyi Ong
- Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Wendy Xueyi Wang
- Program for Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5R 0A3, Canada
| | - Prashanth Komirishetty
- Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Aparna Areti
- Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Ambika Chandrasekhar
- Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Matt Larouche
- Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Julie L Lefebvre
- Program for Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5R 0A3, Canada
| | - Douglas W Zochodne
- Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
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3
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Burek M, Kaupp V, Blecharz-Lang K, Dilling C, Meybohm P. Protocadherin gamma C3: a new player in regulating vascular barrier function. Neural Regen Res 2023. [PMID: 35799511 PMCID: PMC9241426 DOI: 10.4103/1673-5374.343896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Defects in the endothelial cell barrier accompany diverse malfunctions of the central nervous system such as neurodegenerative diseases, stroke, traumatic brain injury, and systemic diseases such as sepsis, viral and bacterial infections, and cancer. Compromised endothelial sealing leads to leaking blood vessels, followed by vasogenic edema. Brain edema as the most common complication caused by stroke and traumatic brain injury is the leading cause of death. Brain microvascular endothelial cells, together with astrocytes, pericytes, microglia, and neurons form a selective barrier, the so-called blood-brain barrier, which regulates the movement of molecules inside and outside of the brain. Mechanisms that regulate blood-brain barrier permeability in health and disease are complex and not fully understood. Several newly discovered molecules that are involved in the regulation of cellular processes in brain microvascular endothelial cells have been described in the literature in recent years. One of these molecules that are highly expressed in brain microvascular endothelial cells is protocadherin gamma C3. In this review, we discuss recent evidence that protocadherin gamma C3 is a newly identified key player involved in the regulation of vascular barrier function.
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4
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Carrier A, Desjobert C, Lobjois V, Rigal L, Busato F, Tost J, Ensenyat-Mendez M, Marzese DM, Pradines A, Favre G, Lamant L, Lanfrancone L, Etievant C, Arimondo PB, Riond J. Epigenetically regulated PCDHB15 impairs aggressiveness of metastatic melanoma cells. Clin Epigenetics 2022; 14:156. [PMID: 36443814 PMCID: PMC9707039 DOI: 10.1186/s13148-022-01364-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/25/2022] [Indexed: 11/29/2022] Open
Abstract
The protocadherin proteins are cell adhesion molecules at the crossroad of signaling pathways playing a major role in neuronal development. It is now understood that their role as signaling hubs is not only important for the normal physiology of cells but also for the regulation of hallmarks of cancerogenesis. Importantly, protocadherins form a cluster of genes that are regulated by DNA methylation. We have identified for the first time that PCDHB15 gene is DNA-hypermethylated on its unique exon in the metastatic melanoma-derived cell lines and patients' metastases compared to primary tumors. This DNA hypermethylation silences the gene, and treatment with the DNA demethylating agent 5-aza-2'-deoxycytidine reinduces its expression. We explored the role of PCDHB15 in melanoma aggressiveness and showed that overexpression impairs invasiveness and aggregation of metastatic melanoma cells in vitro and formation of lung metastasis in vivo. These findings highlight important modifications of the methylation of the PCDHβ genes in melanoma and support a functional role of PCDHB15 silencing in melanoma aggressiveness.
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Affiliation(s)
- Arnaud Carrier
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France ,Cancer Epigenetics Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Cécile Desjobert
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France
| | - Valérie Lobjois
- grid.508721.9Institut des Technologies Avancées en Sciences du Vivant – ITAV-USR3505, CNRS, Université de Toulouse, Université Paul Sabatier-UT3, Toulouse, France ,grid.15781.3a0000 0001 0723 035XLaboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, CNRS UMR 5088, Université Paul Sabatier-UT3, Toulouse, France
| | - Lise Rigal
- grid.508721.9Institut des Technologies Avancées en Sciences du Vivant – ITAV-USR3505, CNRS, Université de Toulouse, Université Paul Sabatier-UT3, Toulouse, France
| | - Florence Busato
- grid.460789.40000 0004 4910 6535Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humain, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, France
| | - Jörg Tost
- grid.460789.40000 0004 4910 6535Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humain, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, France
| | - Miquel Ensenyat-Mendez
- grid.507085.fCancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d’Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Diego M. Marzese
- grid.507085.fCancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d’Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Anne Pradines
- grid.15781.3a0000 0001 0723 035XInserm, CNRS, Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Université Toulouse III-Paul Sabatier, Toulouse, France ,grid.417829.10000 0000 9680 0846Laboratoire de Biologie Médicale Oncologique, Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Gilles Favre
- grid.15781.3a0000 0001 0723 035XInserm, CNRS, Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Université Toulouse III-Paul Sabatier, Toulouse, France ,grid.417829.10000 0000 9680 0846Laboratoire de Biologie Médicale Oncologique, Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Laurence Lamant
- grid.488470.7Laboratoire d’Anatomopathologie, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France
| | - Luisa Lanfrancone
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, Instituto Europeo di Oncologia, Via Adamello 16, 20139 Milan, Italy
| | - Chantal Etievant
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France
| | - Paola B. Arimondo
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France ,grid.428999.70000 0001 2353 6535EpiCBio, Epigenetic Chemical Biology, Department Structural Biology and Chemistry, CNRS UMR N°3523, Institut Pasteur, 28 Rue du Dr Roux, 75015 Paris, France
| | - Joëlle Riond
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France ,grid.15781.3a0000 0001 0723 035XInserm, CNRS, Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Université Toulouse III-Paul Sabatier, Toulouse, France
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5
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Laurent A, Madigou T, Bizot M, Turpin M, Palierne G, Mahé E, Guimard S, Métivier R, Avner S, Le Péron C, Salbert G. TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis. Life Sci Alliance 2022; 5:5/7/e202101283. [PMID: 35351824 PMCID: PMC8963717 DOI: 10.26508/lsa.202101283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
TET2-mediated oxidation of 5-methylcytosine establishes an antiviral state and contributes to MYC-dependent down-regulation of genes involved in lysosome biogenesis and function in breast cancer cells. Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression by controlling the chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs, and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. The TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes that, interestingly, differed in part from the one observed upon treatment with the hypomethylating agent decitabine. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC-binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function. Thus, an extensive cross-talk between TET2 and the oncogenic transcription factor MYC establishes a lysosomal storage disease–like state that contributes to an exacerbated sensitivity to autophagy inducers.
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Affiliation(s)
- Audrey Laurent
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Thierry Madigou
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Maud Bizot
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Marion Turpin
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gaëlle Palierne
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Elise Mahé
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Sarah Guimard
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Raphaël Métivier
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Stéphane Avner
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Christine Le Péron
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gilles Salbert
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
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6
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Legge D, Li L, Moriarty W, Lee D, Szemes M, Zahed A, Panousopoulos L, Chung WY, Aghabi Y, Barratt J, Williams R, Pritchard‐Jones K, Malik KT, Oltean S, Brown KW. The epithelial splicing regulator ESRP2 is epigenetically repressed by DNA hypermethylation in Wilms tumour and acts as a tumour suppressor. Mol Oncol 2022; 16:630-647. [PMID: 34520622 PMCID: PMC8807366 DOI: 10.1002/1878-0261.13101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/04/2021] [Accepted: 09/13/2021] [Indexed: 11/20/2022] Open
Abstract
Wilms tumour (WT), an embryonal kidney cancer, has been extensively characterised for genetic and epigenetic alterations, but a proportion of WTs still lack identifiable abnormalities. To uncover DNA methylation changes critical for WT pathogenesis, we compared the epigenome of foetal kidney with two WT cell lines, filtering our results to remove common cancer-associated epigenetic changes and to enrich for genes involved in early kidney development. This identified four hypermethylated genes, of which ESRP2 (epithelial splicing regulatory protein 2) was the most promising for further study. ESRP2 was commonly repressed by DNA methylation in WT, and this occurred early in WT development (in nephrogenic rests). ESRP2 expression was reactivated by DNA methyltransferase inhibition in WT cell lines. When ESRP2 was overexpressed in WT cell lines, it inhibited cellular proliferation in vitro, and in vivo it suppressed tumour growth of orthotopic xenografts in nude mice. RNA-seq of the ESRP2-expressing WT cell lines identified several novel splicing targets. We propose a model in which epigenetic inactivation of ESRP2 disrupts the mesenchymal to epithelial transition in early kidney development to generate WT.
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Affiliation(s)
- Danny Legge
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | - Ling Li
- Institute of Biomedical & Clinical SciencesUniversity of Exeter Medical SchoolUK
| | - Whei Moriarty
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | - David Lee
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | - Marianna Szemes
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | - Asef Zahed
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | | | - Wan Yun Chung
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | - Yara Aghabi
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | - Jasmin Barratt
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | - Richard Williams
- Cancer SectionUCL Great Ormond Street Institute of Child HealthLondonUK
| | | | - Karim T.A. Malik
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | - Sebastian Oltean
- Institute of Biomedical & Clinical SciencesUniversity of Exeter Medical SchoolUK
| | - Keith W. Brown
- School of Cellular and Molecular MedicineUniversity of BristolUK
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7
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Buccarelli M, Lulli V, Giuliani A, Signore M, Martini M, D'Alessandris QG, Giannetti S, Novelli A, Ilari R, Giurato G, Boe A, Castellani G, Spartano S, Marangi G, Biffoni M, Genuardi M, Pallini R, Marziali G, Ricci-Vitiani L. Deregulated expression of the imprinted DLK1-DIO3 region in glioblastoma stemlike cells: tumor suppressor role of lncRNA MEG3. Neuro Oncol 2021; 22:1771-1784. [PMID: 32459347 PMCID: PMC7746944 DOI: 10.1093/neuonc/noaa127] [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] [Indexed: 12/18/2022] Open
Abstract
Background Glioblastoma (GBM) stemlike cells (GSCs) are thought to be responsible for the maintenance and aggressiveness of GBM, the most common primary brain tumor in adults. This study aims at elucidating the involvement of deregulations within the imprinted delta-like homolog 1 gene‒type III iodothyronine deiodinase gene (DLK-DIO3) region on chromosome 14q32 in GBM pathogenesis. Methods Real-time PCR analyses were performed on GSCs and GBM tissues. Methylation analyses, gene expression, and reverse-phase protein array profiles were used to investigate the tumor suppressor function of the maternally expressed 3 gene (MEG3). Results Loss of expression of genes and noncoding RNAs within the DLK1-DIO3 region was observed in GSCs and GBM tissues compared with normal brain. This downregulation is mainly mediated by epigenetic silencing. Kaplan–Meier analysis indicated that low expression of MEG3 and MEG8 long noncoding (lnc)RNAs significantly correlated with short survival in GBM patients. MEG3 restoration impairs tumorigenic abilities of GSCs in vitro by inhibiting cell growth, migration, and colony formation and decreases in vivo tumor growth, reducing infiltrative growth. These effects were associated with modulation of genes involved in cell adhesion and epithelial-to-mesenchymal transition (EMT). Conclusion In GBM, MEG3 acts as a tumor suppressor mainly regulating cell adhesion, EMT, and cell proliferation, thus providing a potential candidate for novel GBM therapies.
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Affiliation(s)
| | | | | | - Michele Signore
- Core Facilities, Higher Institute of Health (Istituto Superiore di Sanità), Rome, Italy
| | - Maurizio Martini
- A. Gemelli University Polyclinic Foundation, Scientific Hospitalization and Care Institute (IRCCS), Rome, Italy.,Institutes of Pathology, Catholic University School of Medicine, Rome, Italy
| | - Quintino G D'Alessandris
- A. Gemelli University Polyclinic Foundation, Scientific Hospitalization and Care Institute (IRCCS), Rome, Italy.,Neurosurgery, Catholic University School of Medicine, Rome, Italy
| | - Stefano Giannetti
- A. Gemelli University Polyclinic Foundation, Scientific Hospitalization and Care Institute (IRCCS), Rome, Italy.,Human Anatomy, Catholic University School of Medicine, Rome, Italy
| | - Agnese Novelli
- Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Ramona Ilari
- Department of Oncology and Molecular Medicine Rome, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery, and Dentistry, "Scuola Medica Salernitana," University of Salerno, Baronissi, Salerno, Italy.,Genomix4Life Srl, University of Salerno, Baronissi, Salerno, Italy
| | - Alessandra Boe
- Core Facilities, Higher Institute of Health (Istituto Superiore di Sanità), Rome, Italy
| | | | - Serena Spartano
- Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Giuseppe Marangi
- Department of Oncology and Molecular Medicine Rome, Italy.,Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine Rome, Italy
| | - Maurizio Genuardi
- A. Gemelli University Polyclinic Foundation, Scientific Hospitalization and Care Institute (IRCCS), Rome, Italy.,Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Roberto Pallini
- A. Gemelli University Polyclinic Foundation, Scientific Hospitalization and Care Institute (IRCCS), Rome, Italy.,Neurosurgery, Catholic University School of Medicine, Rome, Italy
| | - Giovanna Marziali
- Department of Oncology and Molecular Medicine Rome, Italy.,Genomic Medicine, Catholic University School of Medicine, Rome, Italy
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8
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Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation. Nat Commun 2021; 12:651. [PMID: 33510161 PMCID: PMC7844026 DOI: 10.1038/s41467-020-20849-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia and mantle cell lymphoma patients, here we integrate in situ Hi-C and nine additional omics layers. Beyond conventional active (A) and inactive (B) compartments, we uncover a highly-dynamic intermediate compartment enriched in poised and polycomb-repressed chromatin. During B cell development, 28% of the compartments change, mostly involving a widespread chromatin activation from naive to germinal center B cells and a reversal to the naive state upon further maturation into memory B cells. B cell neoplasms are characterized by both entity and subtype-specific alterations in 3D genome organization, including large chromatin blocks spanning key disease-specific genes. This study indicates that 3D genome interactions are extensively modulated during normal B cell differentiation and that the genome of B cell neoplasias acquires a tumor-specific 3D genome architecture.
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9
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Zhou H, Zheng XD, Lin CM, Min J, Hu S, Hu Y, Li LY, Chen JS, Liu YM, Li HD, Meng XM, Li J, Yang YR, Xu T. Advancement and properties of circular RNAs in prostate cancer: An emerging and compelling frontier for discovering. Int J Biol Sci 2021; 17:651-669. [PMID: 33613119 PMCID: PMC7893591 DOI: 10.7150/ijbs.52266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/18/2020] [Indexed: 01/12/2023] Open
Abstract
Prostate cancer (PC) is the most common carcinoma among men worldwide which results in 26% of leading causes of cancer-related death. However, the ideal and effective molecular marker remains elusive. CircRNA, initially observed in plant-infected viruses and Sendai virus in 1979, is generated from pre-mRNA back-splicing and comes in to play by adequate expression. The differential expression in prostate tissues compared with the control reveals the promising capacity in modulating processes including carcinogenesis and metastasis. However, the biological mechanisms of regulatory network in PC needs to systemically concluded. In this review, we enlightened the comprehensive studies on the definite mechanisms of circRNAs affecting tumor progression and metastasis. What's more, we validated the potential clinical application of circRNAs serving as diagnostic and prognostic biomarker. The discussion and analysis in circRNAs will broaden our knowledge of the pathogenesis of PC and further optimize the current therapies against different condition.
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Affiliation(s)
- Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC West District, University of Science and Technology of China, Hefei 230031, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Xu-Dong Zheng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Chang-Ming Lin
- Department of Urology, the Fourth Affiliated Hospital of Anhui Medical University, Hefei, 230011, China
| | - Jie Min
- Department of Urology, The Second Hospital of Anhui Medical University, Hefei 230601, China
| | - Shuang Hu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Ying Hu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Liang-Yun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Jia-Si Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Yu-Min Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Hao-Dong Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Ya-Ru Yang
- Department of Clinical Trial Research Center, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
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10
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Gabbert L, Dilling C, Meybohm P, Burek M. Deletion of Protocadherin Gamma C3 Induces Phenotypic and Functional Changes in Brain Microvascular Endothelial Cells In Vitro. Front Pharmacol 2020; 11:590144. [PMID: 33390965 PMCID: PMC7774295 DOI: 10.3389/fphar.2020.590144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/09/2020] [Indexed: 01/25/2023] Open
Abstract
Inflammation of the central nervous system (CNS) is associated with diseases such as multiple sclerosis, stroke and neurodegenerative diseases. Compromised integrity of the blood-brain barrier (BBB) and increased migration of immune cells into the CNS are the main characteristics of brain inflammation. Clustered protocadherins (Pcdhs) belong to a large family of cadherin-related molecules. Pcdhs are highly expressed in the CNS in neurons, astrocytes, pericytes and epithelial cells of the choroid plexus and, as we have recently demonstrated, in brain microvascular endothelial cells (BMECs). Knockout of a member of the Pcdh subfamily, PcdhgC3, resulted in significant changes in the barrier integrity of BMECs. Here we characterized the endothelial PcdhgC3 knockout (KO) cells using paracellular permeability measurements, proliferation assay, wound healing assay, inhibition of signaling pathways, oxygen/glucose deprivation (OGD) and a pro-inflammatory cytokine tumor necrosis factor alpha (TNFα) treatment. PcdhgC3 KO showed an increased paracellular permeability, a faster proliferation rate, an altered expression of efflux pumps, transporters, cellular receptors, signaling and inflammatory molecules. Serum starvation led to significantly higher phosphorylation of extracellular signal-regulated kinases (Erk) in KO cells, while no changes in phosphorylated Akt kinase levels were found. PcdhgC3 KO cells migrated faster in the wound healing assay and this migration was significantly inhibited by respective inhibitors of the MAPK-, β-catenin/Wnt-, mTOR- signaling pathways (SL327, XAV939, or Torin 2). PcdhgC3 KO cells responded stronger to OGD and TNFα by significantly higher induction of interleukin 6 mRNA than wild type cells. These results suggest that PcdhgC3 is involved in the regulation of major signaling pathways and the inflammatory response of BMECs.
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Affiliation(s)
- Lydia Gabbert
- Department of Anaesthesia and Critical Care, University of Würzburg, Würzburg, Germany
| | - Christina Dilling
- Department of Anaesthesia and Critical Care, University of Würzburg, Würzburg, Germany
| | - Patrick Meybohm
- Department of Anaesthesia and Critical Care, University of Würzburg, Würzburg, Germany
| | - Malgorzata Burek
- Department of Anaesthesia and Critical Care, University of Würzburg, Würzburg, Germany
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11
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Wu Q, Jia Z. Wiring the Brain by Clustered Protocadherin Neural Codes. Neurosci Bull 2020; 37:117-131. [PMID: 32939695 PMCID: PMC7811963 DOI: 10.1007/s12264-020-00578-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/02/2020] [Indexed: 12/18/2022] Open
Abstract
There are more than a thousand trillion specific synaptic connections in the human brain and over a million new specific connections are formed every second during the early years of life. The assembly of these staggeringly complex neuronal circuits requires specific cell-surface molecular tags to endow each neuron with a unique identity code to discriminate self from non-self. The clustered protocadherin (Pcdh) genes, which encode a tremendous diversity of cell-surface assemblies, are candidates for neuronal identity tags. We describe the adaptive evolution, genomic structure, and regulation of expression of the clustered Pcdhs. We specifically focus on the emerging 3-D architectural and biophysical mechanisms that generate an enormous number of diverse cell-surface Pcdhs as neural codes in the brain.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Joint International Research Laboratory of Metabolic and Developmental Sciences, Institute of Systems Biomedicine, Xinhua Hospital, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhilian Jia
- Center for Comparative Biomedicine, Ministry of Education Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Joint International Research Laboratory of Metabolic and Developmental Sciences, Institute of Systems Biomedicine, Xinhua Hospital, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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12
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Pancho A, Aerts T, Mitsogiannis MD, Seuntjens E. Protocadherins at the Crossroad of Signaling Pathways. Front Mol Neurosci 2020; 13:117. [PMID: 32694982 PMCID: PMC7339444 DOI: 10.3389/fnmol.2020.00117] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/08/2020] [Indexed: 12/25/2022] Open
Abstract
Protocadherins (Pcdhs) are cell adhesion molecules that belong to the cadherin superfamily, and are subdivided into clustered (cPcdhs) and non-clustered Pcdhs (ncPcdhs) in vertebrates. In this review, we summarize their discovery, expression mechanisms, and roles in neuronal development and cancer, thereby highlighting the context-dependent nature of their actions. We furthermore provide an extensive overview of current structural knowledge, and its implications concerning extracellular interactions between cPcdhs, ncPcdhs, and classical cadherins. Next, we survey the known molecular action mechanisms of Pcdhs, emphasizing the regulatory functions of proteolytic processing and domain shedding. In addition, we outline the importance of Pcdh intracellular domains in the regulation of downstream signaling cascades, and we describe putative Pcdh interactions with intracellular molecules including components of the WAVE complex, the Wnt pathway, and apoptotic cascades. Our overview combines molecular interaction data from different contexts, such as neural development and cancer. This comprehensive approach reveals potential common Pcdh signaling hubs, and points out future directions for research. Functional studies of such key factors within the context of neural development might yield innovative insights into the molecular etiology of Pcdh-related neurodevelopmental disorders.
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Affiliation(s)
- Anna Pancho
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Tania Aerts
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuela D Mitsogiannis
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
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13
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Bergholtz H, Lien TG, Swanson DM, Frigessi A, Daidone MG, Tost J, Wärnberg F, Sørlie T. Contrasting DCIS and invasive breast cancer by subtype suggests basal-like DCIS as distinct lesions. NPJ Breast Cancer 2020; 6:26. [PMID: 32577501 PMCID: PMC7299965 DOI: 10.1038/s41523-020-0167-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/20/2020] [Indexed: 12/19/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) is a non-invasive type of breast cancer with highly variable potential of becoming invasive and affecting mortality. Currently, many patients with DCIS are overtreated due to the lack of specific biomarkers that distinguish low risk lesions from those with a higher risk of progression. In this study, we analyzed 57 pure DCIS and 313 invasive breast cancers (IBC) from different patients. Three levels of genomic data were obtained; gene expression, DNA methylation, and DNA copy number. We performed subtype stratified analyses and identified key differences between DCIS and IBC that suggest subtype specific progression. Prominent differences were found in tumors of the basal-like subtype: Basal-like DCIS were less proliferative and showed a higher degree of differentiation than basal-like IBC. Also, core basal tumors (characterized by high correlation to the basal-like centroid) were not identified amongst DCIS as opposed to IBC. At the copy number level, basal-like DCIS exhibited fewer copy number aberrations compared with basal-like IBC. An intriguing finding through analysis of the methylome was hypermethylation of multiple protocadherin genes in basal-like IBC compared with basal-like DCIS and normal tissue, possibly caused by long range epigenetic silencing. This points to silencing of cell adhesion-related genes specifically in IBC of the basal-like subtype. Our work confirms that subtype stratification is essential when studying progression from DCIS to IBC, and we provide evidence that basal-like DCIS show less aggressive characteristics and question the assumption that basal-like DCIS is a direct precursor of basal-like invasive breast cancer.
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Affiliation(s)
- Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tonje G. Lien
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - David M. Swanson
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Arnoldo Frigessi
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Maria Grazia Daidone
- Department of Applied Research and Technical development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Fredrik Wärnberg
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Department of Surgery, Uppsala Academic Hospital, Uppsala, Sweden
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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14
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Li Y, Gong H, Ding J, Zhao F, Du J, Wan J, Zhang J, Liu S, Li J, Wang L, Zhou B. Inhibition of GSK3 Represses the Expression of Retinoic Acid Synthetic Enzyme ALDH1A2 via Wnt/β-Catenin Signaling in WiT49 Cells. Front Cell Dev Biol 2020; 8:94. [PMID: 32258025 PMCID: PMC7092725 DOI: 10.3389/fcell.2020.00094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/04/2020] [Indexed: 02/02/2023] Open
Abstract
Organogenesis, including renal development, requires an appropriate retinoic acid concentration, which is established by differential expression of aldehyde dehydrogenase 1 family member A2 (ALDH1A2) and cytochrome P450 family 26 subfamily A/B/C member 1 (CYP26A1/B1/C1). In the fetal kidney, ALDH1A2 expresses in the developing stroma and renal vesicle and its derivatives but does not present in the ureteric bud. It remains unclear what may contribute to this expression pattern. Here we show that the glycogen synthase kinase 3 alpha/beta (GSK3A/B) inhibitor CHIR99021 significantly represses ALDH1A2 expression in WiT49, which is a Wilms’ tumor cell line that exhibits “triphasic” differential potential and is used as a fetal kidney cell model. CHIR99021 fails to suppress ALDH1A2 as β-catenin is inhibited, suggesting that the downregulation of ALDH1A2 by CHIR99021 is through Wnt/β-catenin signaling. Ectopic expression of mouse Wnt1, Wnt3a, Wnt4, and Wnt9b represses ALDH1A2 expression in WiT49 cells. Using immunohistochemistry, we show an inverse correlation of Aldh1a2 expression with β-catenin in rat E18.5 kidney. ChIP demonstrated that β-catenin is recruited to the ALDH1A2 promoter, the conserved intron1G, and another site within intron 1 of ALDH1A2. Using a luciferase assay, we further show that the ALDH1A2 promoter and the intron1G element are involved in the repression of ALDH1A2 expression by CHIR99021. Our work demonstrates that ALDH1A2 expression can be directly repressed by the Wnt/β-catenin signaling in fetal kidney cells, suggesting that Wnt/β-catenin may play a role in maintaining the expression pattern of ALDH1A2 in the fetal kidney, thus controlling the availability and localization of retinoic acid and regulating aspects of kidney development.
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Affiliation(s)
- Yifan Li
- Central Laboratory, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China.,Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
| | - Hui Gong
- Central Laboratory, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
| | - Jiangfeng Ding
- Department of Stomotology, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
| | - Fujuan Zhao
- Department of Pathology, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
| | - Jihui Du
- Central Laboratory, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Juan Zhang
- Department of Pathology, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
| | - Shaoxiong Liu
- Department of Pathology, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
| | - Jing Li
- Department of Endocrinology, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
| | - Lei Wang
- Central Laboratory, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
| | - Bei Zhou
- Central Laboratory, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University, Shenzhen, China
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15
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Sun R, Xiang T, Tang J, Peng W, Luo J, Li L, Qiu Z, Tan Y, Ye L, Zhang M, Ren G, Tao Q. 19q13 KRAB zinc-finger protein ZNF471 activates MAPK10/JNK3 signaling but is frequently silenced by promoter CpG methylation in esophageal cancer. Theranostics 2020; 10:2243-2259. [PMID: 32089740 PMCID: PMC7019175 DOI: 10.7150/thno.35861] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022] Open
Abstract
Zinc-finger proteins (ZFPs) are the largest transcription factor family in mammals, involved in the regulation of multiple physiologic processes including cell differentiation, proliferation, apoptosis and neoplastic transformation. Approximately one-third of ZFPs are Krüppel-associated box domain (KRAB)-ZFPs. Methods: ZNF471 expression and methylation were detected by reverse-transcription PCR and methylation-specific PCR. The impact and mechanism of ectopic ZNF471 expression in esophageal squamous cell carcinoma (ESCC) cells was evaluated in vitro and in vivo. Results: We identified a 19q13 KRAB-ZFP, ZNF471, as a methylated target in ESCC. We further found that ZNF471 is significantly downregulated in ESCC tissues compared with adjacent non-cancer tissues, due to its aberrant promoter CpG methylation, and further confirmed by methylation analysis and treatment with demethylation agent. Restoration of ZNF471 expression in silenced ESCC cells significantly altered cell morphology, induced apoptosis and G0/G1 arrest, and inhibited tumor cell colony formation, viability, migration and invasion. Importantly, ZNF471 was found to activate the expression of MAPK10/JNK3 and PCDH family genes, and further enhance MAPK10 signaling and downstream gene expression through binding to the MAPK10/JNK3 promoter. Conclusion: Our results demonstrate that ZNF471 is an important tumor suppressor and loss of ZNF471 functions hampers MAPK10/JNK3 signaling during esophageal carcinogenesis.
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16
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Bernardo-Castiñeira C, Valdés N, Celada L, Martinez ASJ, Sáenz-de-Santa-María I, Bayón GF, Fernández AF, Sierra MI, Fraga MF, Astudillo A, Jiménez-Fonseca P, Rial JC, Hevia MÁ, Turienzo E, Bernardo C, Forga L, Tena I, Molina-Garrido MJ, Cacho L, Villabona C, Serrano T, Scola B, Chirivella I, Del Olmo M, Menéndez CL, Navarro E, Tous M, Vallejo A, Athimulam S, Bancos I, Suarez C, Chiara MD. Epigenetic Deregulation of Protocadherin PCDHGC3 in Pheochromocytomas/Paragangliomas Associated With SDHB Mutations. J Clin Endocrinol Metab 2019; 104:5673-5692. [PMID: 31216007 DOI: 10.1210/jc.2018-01471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 06/13/2019] [Indexed: 12/29/2022]
Abstract
CONTEXT SDHB mutations are found in an increasing number of neoplasms, most notably in paragangliomas and pheochromocytomas (PPGLs). SDHB-PPGLs are slow-growing tumors, but ∼50% of them may develop metastasis. The molecular basis of metastasis in these tumors is a long-standing and unresolved problem. Thus, a better understanding of the biology of metastasis is needed. OBJECTIVE This study aimed to identify gene methylation changes relevant for metastatic SDHB-PPGLs. DESIGN We performed genome-wide profiling of DNA methylation in diverse clinical and genetic PPGL subtypes, and validated protocadherin γ-C3 (PCDHGC3) gene promoter methylation in metastatic SDHB-PPGLs. RESULTS We define an epigenetic landscape specific for metastatic SDHB-PPGLs. DNA methylation levels were found significantly higher in metastatic SDHB-PPGLs than in SDHB-PPGLs without metastases. One such change included long-range de novo methylation of the PCDHA, PCDHB, and PCDHG gene clusters. High levels of PCDHGC3 promoter methylation were validated in primary metastatic SDHB-PPGLs, it was found amplified in the corresponding metastases, and it was significantly correlated with PCDHGC3 reduced expression. Interestingly, this epigenetic alteration could be detected in primary tumors that developed metastasis several years later. We also show that PCDHGC3 down regulation engages metastasis-initiating capabilities by promoting cell proliferation, migration, and invasion. CONCLUSIONS Our data provide a map of the DNA methylome episignature specific to an SDHB-mutated cancer and establish PCDHGC3 as a putative suppressor gene and a potential biomarker to identify patients with SDHB-mutated cancer at high risk of metastasis who might benefit from future targeted therapies.
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Affiliation(s)
- Cristóbal Bernardo-Castiñeira
- Head and Neck Oncology Laboratory, Hospital Universitario Central de Asturias, Oviedo, Spain
- Institute of Oncology of Asturias, Spain
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Oncología, Oviedo, Spain
| | - Nuria Valdés
- Service of Endocrinology and Nutrition, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Lucía Celada
- Head and Neck Oncology Laboratory, Hospital Universitario Central de Asturias, Oviedo, Spain
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Oncología, Oviedo, Spain
| | | | - I Sáenz-de-Santa-María
- Head and Neck Oncology Laboratory, Hospital Universitario Central de Asturias, Oviedo, Spain
- Institute of Oncology of Asturias, Spain
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
| | - Gustavo F Bayón
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
- Cancer Epigenetics Laboratory, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Agustín F Fernández
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
- Cancer Epigenetics Laboratory, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Marta I Sierra
- Institute of Oncology of Asturias, Spain
- Cancer Epigenetics Laboratory, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Mario F Fraga
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
- Nanomaterials and Nanotechnology Research Center, Spanish Council for Scientific Research, Universidad de Oviedo, Oviedo, Spain
| | - Aurora Astudillo
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
- Service of Pathology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Paula Jiménez-Fonseca
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
- Service of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Juan Carlos Rial
- Service of Neurosurgery, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Miguel Ángel Hevia
- Service of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Service of Urology Surgery, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Estrella Turienzo
- Service of Surgery, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Carmen Bernardo
- Service of Surgery, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Lluis Forga
- Service of Endocrinology and Nutrition, Complejo Universitario de Navarra, Pamplona, Spain
| | - Isabel Tena
- Service of Medical Oncology, Hospital Provincial de Castellón, Castellón, Spain
| | | | - Laura Cacho
- Service of Endocrinology and Nutrition, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Carles Villabona
- Service of Endocrinology and Nutrition, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Teresa Serrano
- Service of Pathology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Bartolomé Scola
- Service of Head and Neck Surgery, Hospital Gregorio Marañón, Madrid, Spain
| | - Isabel Chirivella
- Unit of Genetic Counsel in Cancer, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Maribel Del Olmo
- Service of Endocrinology and Nutrition, Hospital Universitario La Fe, Valencia, Spain
| | | | - Elena Navarro
- Service of Endocrinology, Hospital Universitario Virgen del Rocío, Seville, Spain
| | - María Tous
- Unidad de Gestión Clínica of Endocrinology and Nutrition, Hospital Virgen Macarena, Seville, Spain
| | - Ana Vallejo
- Unidad de Gestión Clínica of Pathology, Hospital Virgen Macarena, Seville, Spain
| | - Shobana Athimulam
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Mayo Clinic, Rochester, Minnesota
| | - Irina Bancos
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Mayo Clinic, Rochester, Minnesota
| | - Carlos Suarez
- Institute of Oncology of Asturias, Spain
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
| | - María-Dolores Chiara
- Head and Neck Oncology Laboratory, Hospital Universitario Central de Asturias, Oviedo, Spain
- Institute of Oncology of Asturias, Spain
- Institute of Sanitary Research of Principado Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Oncología, Oviedo, Spain
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17
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Lorente-Sorolla C, Garcia-Gomez A, Català-Moll F, Toledano V, Ciudad L, Avendaño-Ortiz J, Maroun-Eid C, Martín-Quirós A, Martínez-Gallo M, Ruiz-Sanmartín A, Del Campo ÁG, Ferrer-Roca R, Ruiz-Rodriguez JC, Álvarez-Errico D, López-Collazo E, Ballestar E. Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis. Genome Med 2019; 11:66. [PMID: 31665078 PMCID: PMC6820973 DOI: 10.1186/s13073-019-0674-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/07/2019] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Sepsis, a life-threatening organ dysfunction caused by a dysregulated systemic immune response to infection, associates with reduced responsiveness to subsequent infections. How such tolerance is acquired is not well understood but is known to involve epigenetic and transcriptional dysregulation. METHODS Bead arrays were used to compare global DNA methylation changes in patients with sepsis, non-infectious systemic inflammatory response syndrome, and healthy controls. Bioinformatic analyses were performed to dissect functional reprogramming and signaling pathways related to the acquisition of these specific DNA methylation alterations. Finally, in vitro experiments using human monocytes were performed to test the induction of similar DNA methylation reprogramming. RESULTS Here, we focused on DNA methylation changes associated with sepsis, given their potential role in stabilizing altered phenotypes. Tolerized monocytes from patients with sepsis display changes in their DNA methylomes with respect to those from healthy controls, affecting critical monocyte-related genes. DNA methylation profiles correlate with IL-10 and IL-6 levels, significantly increased in monocytes in sepsis, as well as with the Sequential Organ Failure Assessment score; the observed changes associate with TFs and pathways downstream to toll-like receptors and inflammatory cytokines. In fact, in vitro stimulation of toll-like receptors in monocytes results in similar gains and losses of methylation together with the acquisition of tolerance. CONCLUSION We have identified a DNA methylation signature associated with sepsis that is downstream to the response of monocytes to inflammatory signals associated with the acquisition of a tolerized phenotype and organic dysfunction.
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Affiliation(s)
- Clara Lorente-Sorolla
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Antonio Garcia-Gomez
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Víctor Toledano
- Innate Immunity Group, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain.,Emergency Department, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain.,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - José Avendaño-Ortiz
- Innate Immunity Group, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain.,Emergency Department, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain
| | - Charbel Maroun-Eid
- Innate Immunity Group, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain
| | | | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group Vall d'Hebron Research Institute (VHIR), 08035, Barcelona, Spain
| | - Adolfo Ruiz-Sanmartín
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d' Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Álvaro García Del Campo
- Cardiac Post-Surgery Unit (UPCC), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Ricard Ferrer-Roca
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d' Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodriguez
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d' Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Damiana Álvarez-Errico
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain
| | - Eduardo López-Collazo
- Innate Immunity Group, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain.,Tumor Immunology Lab, IdiPAZ, La Paz University Hospital, 28046, Madrid, Spain.,Center for Biomedical Research Network, CIBEres, Madrid, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Barcelona, Spain. .,Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
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18
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Shang BQ, Li ML, Quan HY, Hou PF, Li ZW, Chu SF, Zheng JN, Bai J. Functional roles of circular RNAs during epithelial-to-mesenchymal transition. Mol Cancer 2019; 18:138. [PMID: 31526370 PMCID: PMC6745795 DOI: 10.1186/s12943-019-1071-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
Cancer has become a major health issue worldwide, contributing to a high mortality rate. Tumor metastasis is attributed to the death of most patients. Epithelial-to-mesenchymal transition (EMT) plays a vital role in inducing metastasis. During EMT, epithelial cells lose their characteristics, such as cell-to-cell adhesion and cell polarity, and cells gain motility, migratory potential, and invasive properties to become mesenchymal stem cells. Circular RNAs (circRNAs) are closely associated with tumor metastasis and patient prognosis, as revealed by increasing lines of evidence. CircRNA is a type of single-stranded RNA that forms a covalently closed continuous loop. CircRNAs are insensitive to ribonucleases and are widespread in body fluids. This work is the first review on EMT-related circRNAs. In this review, we briefly discuss the characteristics and functions of circRNAs. The correlation of circRNAs with EMT has been reported, and we discuss the ways circRNAs can regulate EMT progression through EMT transcription factors, EMT-related signaling pathways, and other mechanisms. This work summarizes current studies on EMT-related circRNAs in various cancers and provides a theoretical basis for the use of EMT-related circRNAs in targeted management and therapy.
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Affiliation(s)
- Bing-Qing Shang
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Min-Le Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Hao-Yu Quan
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Ping-Fu Hou
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Zhong-Wei Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Su-Fang Chu
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Jun-Nian Zheng
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China.
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China.
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19
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Vega-Benedetti AF, Loi E, Moi L, Blois S, Fadda A, Antonelli M, Arcella A, Badiali M, Giangaspero F, Morra I, Columbano A, Restivo A, Zorcolo L, Gismondi V, Varesco L, Bellomo SE, Giordano S, Canale M, Casadei-Gardini A, Faloppi L, Puzzoni M, Scartozzi M, Ziranu P, Cabras G, Cocco P, Ennas MG, Satta G, Zucca M, Canzio D, Zavattari P. Clustered protocadherins methylation alterations in cancer. Clin Epigenetics 2019; 11:100. [PMID: 31288858 PMCID: PMC6617643 DOI: 10.1186/s13148-019-0695-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/11/2019] [Indexed: 01/29/2023] Open
Abstract
Background Clustered protocadherins (PCDHs) map in tandem at human chromosome 5q31 and comprise three multi-genes clusters: α-, β- and γ-PCDH. The expression of this cluster consists of a complex mechanism involving DNA hub formation through DNA-CCTC binding factor (CTCF) interaction. Methylation alterations can affect this interaction, leading to transcriptional dysregulation. In cancer, clustered PCDHs undergo a mechanism of long-range epigenetic silencing by hypermethylation. Results In this study, we detected frequent methylation alterations at CpG islands associated to these clustered PCDHs in all the solid tumours analysed (colorectal, gastric and biliary tract cancers, pilocytic astrocytoma), but not hematologic neoplasms such as chronic lymphocytic leukemia. Importantly, several altered CpG islands were associated with CTCF binding sites. Interestingly, our analysis revealed a hypomethylation event in pilocytic astrocytoma, suggesting that in neuronal tissue, where PCDHs are highly expressed, these genes become hypomethylated in this type of cancer. On the other hand, in tissues where PCDHs are lowly expressed, these CpG islands are targeted by DNA methylation. In fact, PCDH-associated CpG islands resulted hypermethylated in gastrointestinal tumours. Conclusions Our study highlighted a strong alteration of the clustered PCDHs methylation pattern in the analysed solid cancers and suggested these methylation aberrations in the CpG islands associated with PCDH genes as powerful diagnostic biomarkers. Electronic supplementary material The online version of this article (10.1186/s13148-019-0695-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Sylvain Blois
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Antonio Fadda
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Manila Antonelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy
| | | | - Manuela Badiali
- Genetic and Genomic Laboratory, Microcitemico Children's Hospital, Cagliari, Italy
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy.,IRCCS Neuromed, Pozzilli, Italy
| | - Isabella Morra
- Department of Pathology OIRM-S, Anna Hospital, A.O.U. City of Health and Science, Turin, Italy
| | - Amedeo Columbano
- Department of Biomedical Sciences, Unit of Oncology and Molecular Pathology, University of Cagliari, Cagliari, Italy
| | - Angelo Restivo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Luigi Zorcolo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Liliana Varesco
- Unit of Hereditary Cancer, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Silvia Giordano
- Department of Oncology, University of Turin, Turin, Italy.,Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Matteo Canale
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Andrea Casadei-Gardini
- Department of Medical and Surgical Sciences for Children and Adults, Division of Medical Oncology, Policlinico di Modena Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
| | - Luca Faloppi
- Department of Medical Oncology, University Hospital of Cagliari, Cagliari, Italy.,Medical Oncology Unit, Macerata General Hospital, ASUR Marche AV3, Macerata, Italy
| | - Marco Puzzoni
- Department of Medical Oncology, University Hospital of Cagliari, Cagliari, Italy
| | - Mario Scartozzi
- Department of Medical Oncology, University Hospital of Cagliari, Cagliari, Italy
| | - Pina Ziranu
- Department of Medical Oncology, University Hospital of Cagliari, Cagliari, Italy
| | | | - Pierluigi Cocco
- Department of Medical Sciences and Public Health, Occupational Health Unit, University of Cagliari, Cagliari, Italy
| | - Maria Grazia Ennas
- Department of Biomedical Sciences, Cytomorphology Unit, University of Cagliari, Cagliari, Italy
| | - Giannina Satta
- Department of Medical Sciences and Public Health, Occupational Health Unit, University of Cagliari, Cagliari, Italy
| | - Mariagrazia Zucca
- Department of Biomedical Sciences, Cytomorphology Unit, University of Cagliari, Cagliari, Italy
| | - Daniele Canzio
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy.
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20
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FOSB⁻PCDHB13 Axis Disrupts the Microtubule Network in Non-Small Cell Lung Cancer. Cancers (Basel) 2019; 11:cancers11010107. [PMID: 30658436 PMCID: PMC6357195 DOI: 10.3390/cancers11010107] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 12/31/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is among the leading causes of human mortality. One reason for high rates of NSCLC mortality is that drug resistance is a major problem for both conventional chemotherapies and less-toxic targeted therapies. Thus, novel mechanistic insights into disease pathogenesis may benefit the development of urgently needed therapies. Here we show that FBJ murine osteosarcoma viral oncogene homolog B (FOSB) was induced by an antimicrobial peptide, tilapia piscidin-4 (TP4), through the dysregulation of mitochondrial Ca2+ homeostasis in NSCLC cells. Transcriptomic, chromatin immunoprecipitation quantitative PCR, and immunocytochemical studies reveal that protocadherin-β13 (PCDHB13) as a target of FOSB that was functionally associated with microtubule. Overexpression of either PCDHB13 or FOSB attenuated NSCLC growth and survival in vitro and in vivo. Importantly, downregulation of both FOSB and PCDHB13 was observed in NSCLC patients and was negatively correlated with pathological grade. These findings introduce the FOSB⁻PCDHB13 axis as a novel tumor suppressive pathway in NSCLC.
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21
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Yang Z, Qu CB, Zhang Y, Zhang WF, Wang DD, Gao CC, Ma L, Chen JS, Liu KL, Zheng B, Zhang XH, Zhang ML, Wang XL, Wen JK, Li W. Dysregulation of p53-RBM25-mediated circAMOTL1L biogenesis contributes to prostate cancer progression through the circAMOTL1L-miR-193a-5p-Pcdha pathway. Oncogene 2018; 38:2516-2532. [PMID: 30531834 PMCID: PMC6484770 DOI: 10.1038/s41388-018-0602-8] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/31/2018] [Accepted: 10/31/2018] [Indexed: 01/16/2023]
Abstract
p53, circRNAs and miRNAs are important components of the regulatory network that activates the EMT program in cancer metastasis. In prostate cancer (PCa), however, it has not been investigated whether and how p53 regulates EMT by circRNAs and miRNAs. Here we show that a Amotl1-derived circRNA, termed circAMOTL1L, is downregulated in human PCa, and that decreased circAMOTL1L facilitates PCa cell migration and invasion through downregulating E-cadherin and upregulating vimentin, thus leading to EMT and PCa progression. Mechanistically, we demonstrate that circAMOTL1L serves as a sponge for binding miR-193a-5p in PCa cells, relieving miR-193a-5p repression of Pcdha gene cluster (a subset of the cadherin superfamily members). Accordingly, dysregulation of the circAMOTL1L-miR-193a-5p-Pcdha8 regulatory pathway mediated by circAMOTL1L downregulation contributes to PCa growth in vivo. Further, we show that RBM25 binds directly to circAMOTL1L and induces its biogenesis, whereas p53 regulates EMT via direct activation of RBM25 gene. These findings have linked p53/RBM25-mediated circAMOTL1L-miR-193a-5p-Pcdha regulatory axis to EMT in metastatic progression of PCa. Targeting this newly identified regulatory axis provides a potential therapeutic strategy for aggressive PCa.
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Affiliation(s)
- Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.,Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China.,Department of Science and Technology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chang-Bao Qu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Yong Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Wen-Feng Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Dan-Dan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chun-Cheng Gao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Long Ma
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Jin-Suo Chen
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Kai-Long Liu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Bin Zheng
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Xin-Hua Zhang
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Man-Li Zhang
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China.,Department of Emergency Medicine, The second hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, China
| | - Xiao-Lu Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
| | - Jin-Kun Wen
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China.
| | - Wei Li
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
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22
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Kim S, Wyckoff J, Morris AT, Succop A, Avery A, Duncan GE, Jazwinski SM. DNA methylation associated with healthy aging of elderly twins. GeroScience 2018; 40:469-484. [PMID: 30136078 PMCID: PMC6294724 DOI: 10.1007/s11357-018-0040-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/09/2018] [Indexed: 12/21/2022] Open
Abstract
Variation in healthy aging and lifespan is ascribed more to various non-genetic factors than to inherited genetic determinants, and a major goal in aging research is to reveal the epigenetic basis of aging. One approach to this goal is to find genomic sites or regions where DNA methylation correlates with biological age. Using health data from 134 elderly twins, we calculated a frailty index as a quantitative indicator of biological age, and by applying the Infinium HumanMethylation450K BeadChip technology to their leukocyte DNA samples, we obtained quantitative DNA methylation data on genome-wide CpG sites. We analyzed the health and epigenome data by taking two independent associative approaches: the parametric regression-based approach and a non-parametric machine learning approach followed by GO ontology analysis. Our results indicate that DNA methylation at CpG sites in the promoter region of PCDHGA3 is associated with biological age. PCDHGA3 belongs to clustered protocadherin genes, which are all located in a single locus on chromosome 5 in human. Previous studies of the clustered protocadherin genes showed that (1) DNA methylation is associated with age or age-related phenotypes; (2) DNA methylation can modulate gene expression; (3) dysregulated gene expression is associated with various pathologies; and (4) DNA methylation patterns at this locus are associated with adverse lifetime experiences. All these observations suggest that DNA methylation at the clustered protocadherin genes, including PCDHGA3, is a key mediator of healthy aging.
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Affiliation(s)
- Sangkyu Kim
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA.
| | - Jennifer Wyckoff
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Anne-T Morris
- Virginia Commonwealth University, Mid-Atlantic Twin Registry, Richmond, VA, USA
| | | | - Ally Avery
- University of Washington Twin Registry, Seattle, WA, USA
- Washington State Twin Registry, Washington State University - Health Sciences Spokane, Spokane, WA, USA
| | - Glen E Duncan
- University of Washington Twin Registry, Seattle, WA, USA
- Washington State Twin Registry, Washington State University - Health Sciences Spokane, Spokane, WA, USA
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
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23
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Xue J, Gharaibeh RZ, Pietryk EW, Brouwer C, Tarantino LM, Valdar W, Ideraabdullah FY. Impact of vitamin D depletion during development on mouse sperm DNA methylation. Epigenetics 2018; 13:959-974. [PMID: 30239288 DOI: 10.1080/15592294.2018.1526027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Suboptimal environmental conditions during development can substantially alter the epigenome. Stable environmentally-induced changes to the germline epigenome, in particular, have important implications for the health of the next generation. We showed previously that developmental vitamin D depletion (DVD) resulted in loss of DNA methylation at several imprinted loci over two generations. Here, we assessed the impact of DVD on genome-wide methylation in mouse sperm in order to characterize the number, extent and distribution of methylation changes in response to DVD and to find genes that may be susceptible to this prevalent environmental perturbation. We detected 15,827 loci that were differentially methylated in DVD mouse sperm vs. controls. Most epimutations (69%) were loss of methylation, and the extent of methylation change and number of CpGs affected in a region were associated with genic location and baseline methylation state. Methylation response to DVD at validated loci was only detected in offspring that exhibited a phenotypic response to DVD (increased body and testes weight) suggesting the two types of responses are linked, though a causal relationship is unclear. Epimutations localized to regions enriched for developmental and metabolic genes and pathway analyses showed enrichment for Cadherin, Wnt, PDGF and Integrin signaling pathways. These findings show for the first time that vitamin D status during development leads to substantial DNA methylation changes across the sperm genome and that locus susceptibility is linked to genomic and epigenomic context.
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Affiliation(s)
- Jing Xue
- a Department of Genetics, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA
| | - Raad Z Gharaibeh
- c Department of Bioinformatics and Genomics , University of North Carolina at Charlotte , Charlotte , NC , USA.,d UNC Charlotte Bioinformatics Service Division , North Carolina Research Campus , Kannapolis , NC , USA.,e Department of Medicine, Division of Gastroenterology , University of Florida , Gainesville , FL , USA
| | - Edward W Pietryk
- a Department of Genetics, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA
| | - Cory Brouwer
- c Department of Bioinformatics and Genomics , University of North Carolina at Charlotte , Charlotte , NC , USA.,d UNC Charlotte Bioinformatics Service Division , North Carolina Research Campus , Kannapolis , NC , USA
| | - Lisa M Tarantino
- b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA.,f Department of Psychiatry, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,g Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - William Valdar
- b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA.,h Lineberger Comprehensive Cancer Center , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - Folami Y Ideraabdullah
- a Department of Genetics, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,b Nutrition Research Institute , University of North Carolina at Chapel Hill , Kannapolis , NC , USA.,i Department of Nutrition, Gillings School of Public Health , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
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24
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Wu S, Zhang Y, Zhang L, Ma JL, Zhou T, Li ZX, Liu WD, Li WQ, You WC, Pan KF. Methylation and Expression of Nonclustered Protocadherins Encoding Genes and Risk of Precancerous Gastric Lesions in a High-Risk Population. Cancer Prev Res (Phila) 2018; 11:717-726. [PMID: 30213786 DOI: 10.1158/1940-6207.capr-18-0119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/01/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022]
Abstract
Nonclustered protocadherins (PCDH) family is a group of cell-cell adhesion molecules. We have found differentially methylated genes in the nonclustered PCDHs family associated with Helicobacter pylori (H. pylori) infection in prior genome-wide methylation analysis. To further investigate the methylation and expression of nonclustered PCDHs encoding genes in H. pylori--related gastric carcinogenesis process, four candidate genes including PCDH7, PCDH10, PCDH17, and PCDH20 were selected, which were reported to be tumor suppressors for digestive cancers. A total of 747 participants with a spectrum of gastric lesions were enrolled from a high-risk population of gastric cancer. Promoter methylation levels of four genes were significantly higher in H. pylori-positive subjects than the negative group (all P < 0.001). Elevated methylation levels of PCDH10 and PCDH17 were observed with the increasing severity of gastric lesions (both P trend < 0.001). In the protein expression analysis, PCDH17 expression was inversely associated with gastric lesions; the OR [95% confidence interval (CI)] was 0.49 (0.26-0.95) for chronic atrophic gastritis (CAG), 0.31 (0.15-0.63) for intestinal metaplasia, and 0.38 (0.19-0.75) for indefinite dysplasia and dysplasia, compared with superficial gastritis. In addition, PCDH10 expression was significantly lower in CAG (OR, 0.40; 95% CI, 0.24-0.68). The inverse association between methylation and protein expression of PCDH10 and PCDH17 was further supported when we explored the methylation and mRNA expression in The Cancer Genome Atlas database (all P < 0.001). Our study found elevated promoter methylation and decreased expression of PCDH10 and PCDH17 in advanced gastric lesions, suggesting that elevated PCDH10 and PCDH17 methylation may be an early event in gastric carcinogenesis. Cancer Prev Res; 11(11); 717-26. ©2018 AACR.
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Affiliation(s)
- Si Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Yang Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Lian Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Jun-Ling Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Tong Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Zhe-Xuan Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Wei-Dong Liu
- Linqu Public Health Bureau, Linqu, Shandong, People's Republic of China
| | - Wen-Qing Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Wei-Cheng You
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China.
| | - Kai-Feng Pan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China.
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25
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Alaraudanjoki VK, Koivisto S, Pesonen P, Männikkö M, Leinonen J, Tjäderhane L, Laitala ML, Lussi A, Anttonen VAM. Genome-Wide Association Study of Erosive Tooth Wear in a Finnish Cohort. Caries Res 2018; 53:49-59. [PMID: 29898447 DOI: 10.1159/000488208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/25/2018] [Indexed: 11/19/2022] Open
Abstract
Erosive tooth wear is defined as irreversible loss of dental tissues due to intrinsic or extrinsic acids, exacerbated by mechanical forces. Recent studies have suggested a higher prevalence of erosive tooth wear in males, as well as a genetic contribution to susceptibility to erosive tooth wear. Our aim was to examine erosive tooth wear by performing a genome-wide association study (GWAS) in a sample of the Northern Finland Birth Cohort 1966 (n = 1,962). Erosive tooth wear was assessed clinically using the basic erosive wear examination. A GWAS was performed for the whole sample as well as separately for males and females. We identified one genome-wide significant signal (rs11681214) in the GWAS of the whole sample near the genes PXDN and MYT1L. When the sample was stratified by sex, the strongest genome-wide significant signals were observed in or near the genes FGFR1, C8orf86, CDH4, SCD5, F2R, and ING1. Additionally, multiple suggestive association signals were detected in all GWASs performed. Many of the signals were in or near the genes putatively related to oral environment or tooth development, and some were near the regions considered to be associated with dental caries, such as 2p24, 4q21, and 13q33. Replications of these associations in other samples, as well as experimental studies to determine the biological functions of associated genetic variants, are needed.
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Affiliation(s)
| | - Salla Koivisto
- Research Unit of Oral Health Sciences, University of Oulu, Oulu, Finland
| | - Paula Pesonen
- Northern Finland Birth Cohorts, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Minna Männikkö
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Jukka Leinonen
- Research Unit of Oral Health Sciences, University of Oulu, Oulu, Finland
| | - Leo Tjäderhane
- Research Unit of Oral Health Sciences, University of Oulu, Oulu, Finland.,Northern Finland Birth Cohorts, Faculty of Medicine, University of Oulu, Oulu, Finland.,Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Adrian Lussi
- Department of Preventive, Restorative and Pediatric Dentistry, University of Bern, Bern, Switzerland
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26
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Jeong IB, Yoon YS, Park SY, Cha EJ, Na MJ, Kwon SJ, Kim JH, Oh TJ, An S, Park CR, Kim YJ, Park DH, Son JW. PCDHGA12 methylation biomarker in bronchial washing specimens as an adjunctive diagnostic tool to bronchoscopy in lung cancer. Oncol Lett 2018; 16:1039-1045. [PMID: 29963180 DOI: 10.3892/ol.2018.8699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 11/07/2017] [Indexed: 12/13/2022] Open
Abstract
The use of bronchoscopy is central to the diagnosis of lung cancer. However, the sensitivity of bronchoscopy is low. In addition, bronchial washing cytology, which is a routine adjunctive test, does not significantly improve the performance of bronchoscopy owing to its low sensitivity. To enhance the diagnostic performance of bronchoscopy, the protocadherin GA12 (PCDHGA12) methylation biomarker in bronchial washings was introduced as a novel adjunctive diagnostic test. A total of 98 patients who underwent bronchoscopy owing to suspicion of lung cancer were analyzed. Cytological examination and PCDHGA12 methylation biomarker testing of the bronchial washing fluid were performed. The performance of the tests was analyzed. The final diagnosis in 60 patients was lung cancer and in 38 patients was benign disease. The PCDHGA12 methylation biomarker had a sensitivity of 75.0%, a specificity of 78.9% and a positive predictive value (PPV) of 84.9%, whereas cytological assessment had a sensitivity of 45.0%, a specificity of 92.1% and a PPV of 90%. Patients with positive PCDHGA12 methylation test had an odds ratio for lung cancer of 11.25 (confidence interval, 4.25-29.8) compared with negative subjects. The combination of the two tests exhibited an increased sensitivity (83.3%), a specificity of 71.1% and a PPV of 82.0%. Furthermore, considering the non-diagnostic bronchoscopy group alone, the test demonstrated a sensitivity of 61.9% and a specificity of 78.9%. The results of the present study demonstrated that PCDHGA12 methylation, as a lung cancer biomarker in bronchial washings, may be a used as an adjunctive test to bronchoscopy.
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Affiliation(s)
- In Beom Jeong
- Department of Internal Medicine, Konyang University College of Medicine, Daejeon 35365, Republic of Korea
| | - Yoo Sang Yoon
- Department of Thoracic and Cardiovascular Surgery, Dongnam Institute of Radiological and Medical Sciences, Pusan 46033, Republic of Korea
| | - Shin Young Park
- Department of Pathology, Konyang University College of Medicine, Daejeon 34027, Republic of Korea
| | - Eun Jung Cha
- Department of Pathology, Konyang University College of Medicine, Daejeon 34027, Republic of Korea
| | - Moon Jun Na
- Department of Internal Medicine, Konyang University College of Medicine, Daejeon 35365, Republic of Korea
| | - Sun Jung Kwon
- Department of Internal Medicine, Konyang University College of Medicine, Daejeon 35365, Republic of Korea
| | - Ji Hye Kim
- Department of Internal Medicine, Konyang University College of Medicine, Daejeon 35365, Republic of Korea
| | - Tae Jeong Oh
- Genomictree, Inc., Daejeon 34027, Republic of Korea
| | - Sungwhan An
- Genomictree, Inc., Daejeon 34027, Republic of Korea
| | - Chang Ryul Park
- Department of Cardiothoracic Surgery, Ulsan University Hospital, Ulsan 44033, Republic of Korea
| | - Young Jin Kim
- Department of Thoracic Surgery, Konyang University College of Medicine, Daejeon 35233, Republic of Korea
| | - Dong Ho Park
- Department of Anesthesiology and Pain Medicine, Eulji University College of Medicine, Daejeon 35233, Republic of Korea
| | - Ji Woong Son
- Department of Internal Medicine, Konyang University College of Medicine, Daejeon 35365, Republic of Korea.,Konyang University Myunggok Medical Research Institute, Daejeon 35365, Republic of Korea
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27
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Aref-Eshghi E, Schenkel LC, Ainsworth P, Lin H, Rodenhiser DI, Cutz JC, Sadikovic B. Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues. Front Oncol 2018; 8:100. [PMID: 29740534 PMCID: PMC5925605 DOI: 10.3389/fonc.2018.00100] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/21/2018] [Indexed: 01/27/2023] Open
Abstract
Introduction The current methodology involving diagnosis of prostate cancer (PCa) relies on the pathology examination of prostate needle biopsies, a method with high false negative rates partly due to temporospatial, molecular, and morphological heterogeneity of prostate adenocarcinoma. It is postulated that molecular markers have a potential to assign diagnosis to a considerable portion of undetected prostate tumors. This study examines the genome-wide DNA methylation changes in PCa in search of genomic markers for the development of a diagnostic algorithm for PCa screening. Methods Archival PCa and normal tissues were assessed using genomic DNA methylation arrays. Differentially methylated sites and regions (DMRs) were used for functional assessment, gene-set enrichment and protein interaction analyses, and examination of transcription factor-binding patterns. Raw signal intensity data were used for identification of recurrent copy number variations (CNVs). Non-redundant fully differentiating cytosine-phosphate-guanine sites (CpGs), which did not overlap CNV segments, were used in an L1 regularized logistic regression model (LASSO) to train a classification algorithm. Validation of this algorithm was performed using a large external cohort of benign and tumor prostate arrays. Results Approximately 6,000 probes and 600 genomic regions showed significant DNA methylation changes, primarily involving hypermethylation. Gene-set enrichment and protein interaction analyses found an overrepresentation of genes related to cell communications, neurogenesis, and proliferation. Motif enrichment analysis demonstrated enrichment of tumor suppressor-binding sites nearby DMRs. Several of these regions were also found to contain copy number amplifications. Using four non-redundant fully differentiating CpGs, we trained a classification model with 100% accuracy in discriminating tumors from benign samples. Validation of this algorithm using an external cohort of 234 tumors and 92 benign samples yielded 96% sensitivity and 98% specificity. The model was found to be highly sensitive to detect metastatic lesions in bone, lymph node, and soft tissue, while being specific enough to differentiate the benign hyperplasia of prostate from tumor. Conclusion A considerable component of PCa DNA methylation profile represent driver events potentially established/maintained by disruption of tumor suppressor activity. As few as four CpGs from this profile can be used for screening of PCa.
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Affiliation(s)
- Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - David I Rodenhiser
- Department of Pediatrics, Western University and Children's Health Research Institute, London, ON, Canada.,Department of Biochemistry, Western University and Children's Health Research Institute, London, ON, Canada.,Department of Oncology, Western University and Children's Health Research Institute, London, ON, Canada
| | - Jean-Claude Cutz
- Department of Pathology and Laboratory Medicine, McMaster University, Hamilton, ON, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
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28
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Fadda A, Gentilini D, Moi L, Barault L, Leoni VP, Sulas P, Zorcolo L, Restivo A, Cabras F, Fortunato F, Zavattari C, Varesco L, Gismondi V, De Miglio MR, Scanu AM, Colombi F, Lombardi P, Sarotto I, Loi E, Leone F, Giordano S, Di Nicolantonio F, Columbano A, Zavattari P. Colorectal cancer early methylation alterations affect the crosstalk between cell and surrounding environment, tracing a biomarker signature specific for this tumor. Int J Cancer 2018. [PMID: 29542109 DOI: 10.1002/ijc.31380] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) develops through the accumulation of both genetic and epigenetic alterations. However, while the former are already used as prognostic and predictive biomarkers, the latter are less well characterized. Here, performing global methylation analysis on both CRCs and adenomas by Illumina Infinium HumanMethylation450 Bead Chips, we identified a panel of 74 altered CpG islands, demonstrating that the earliest methylation alterations affect genes coding for proteins involved in the crosstalk between cell and surrounding environment. The panel discriminates CRCs and adenomas from peritumoral and normal mucosa with very high specificity (100%) and sensitivity (99.9%). Interestingly, over 70% of the hypermethylated islands resulted in downregulation of gene expression. To establish the possible usefulness of these non-invasive markers for detection of colon cancer, we selected three biomarkers and identified the presence of altered methylation in stool DNA and plasma cell-free circulating DNA from CRC patients.
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Affiliation(s)
- Antonio Fadda
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Loredana Moi
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Ludovic Barault
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Vera Piera Leoni
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Pia Sulas
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Luigi Zorcolo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Angelo Restivo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Francesco Cabras
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Federica Fortunato
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | | | - Liliana Varesco
- Unit of Hereditary Cancer, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer, IRCCS AOU San Martino-IST, Genoa, Italy
| | | | - Antonio Mario Scanu
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | | | | | - Ivana Sarotto
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Eleonora Loi
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Francesco Leone
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Silvia Giordano
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Amedeo Columbano
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Patrizia Zavattari
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
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29
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Men C, Chai H, Song X, Li Y, Du H, Ren Q. Identification of DNA methylation associated gene signatures in endometrial cancer via integrated analysis of DNA methylation and gene expression systematically. J Gynecol Oncol 2018; 28:e83. [PMID: 29027401 PMCID: PMC5641533 DOI: 10.3802/jgo.2017.28.e83] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/02/2017] [Accepted: 08/10/2017] [Indexed: 12/22/2022] Open
Abstract
Objective Endometrial cancer (EC) is a common gynecologic cancer worldwide. However, the pathogenesis of EC has not been epigenetically elucidated. Here, this study aims to describe the DNA methylation profile and identify favorable gene signatures highly associated with aberrant DNA methylation changes in EC. Methods The data regarding DNA methylation and gene expression were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially methylated CpG sites (DMCs), differentially methylated regions (DMRs), and differentially expressed genes (DEGs) were identified, and the relationship between the 2 omics was further analyzed. In addition, weighted CpG site co-methylation network (WCCN) was constructed followed by an integrated analysis of DNA methylation and gene expression data. Results Four hundred thirty-one tumor tissues and 46 tissues adjacent tumor of EC patients were analyzed. One thousand one hundred thirty-five DMCs (merging to 10 DMRs), and 1,488 DEGs were obtained between tumor and normal groups, respectively. One hundred forty-eight DMCs-DEGs correlated pairs and 13 regional DMCs-DEGs pairs were obtained. Interestingly, we found that some hub genes in 2 modules among 8 modules of WCCN analysis were down-regulated in tumor samples. Furthermore, protocadherins (PCDHs) clusters, DDP6, TNXB, and ZNF154 were identified as novel deregulated genes with altered methylation in EC. Conclusion Based on the analysis of DNA methylation in a systematic view, the potential long-range epigenetic silencing (LRES) composed of PCDHs was reported in ECs for the first time. PCDHs clusters, DDP6, and TNXB were firstly found to be associated with tumorigenesis, and may be novel candidate biomarkers for EC.
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Affiliation(s)
- Chuandi Men
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Graduate School, Bengbu Medical College, Bengbu, China
| | - Hongjuan Chai
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xumin Song
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Li
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huawen Du
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Ren
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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30
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Dilling C, Roewer N, Förster CY, Burek M. Multiple protocadherins are expressed in brain microvascular endothelial cells and might play a role in tight junction protein regulation. J Cereb Blood Flow Metab 2017; 37:3391-3400. [PMID: 28094605 PMCID: PMC5624389 DOI: 10.1177/0271678x16688706] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protocadherins (Pcdhs) are a large family of cadherin-related molecules. They play a role in cell adhesion, cellular interactions, and development of the central nervous system. However, their expression and role in endothelial cells has not yet been characterized. Here, we examined the expression of selected clustered Pcdhs in endothelial cells from several vascular beds. We analyzed human and mouse brain microvascular endothelial cell (BMEC) lines and primary cells, mouse myocardial microvascular endothelial cell line, and human umbilical vein endothelial cells. We examined the mRNA and protein expression of selected Pcdhs using RT-PCR, Western blot, and immunostaining. A strong mRNA expression of Pcdhs was observed in all endothelial cells tested. At the protein level, Pcdhs-gamma were detected using an antibody against the conserved C-terminal domain of Pcdhs-gamma or an antibody against PcdhgC3. Deletion of highly expressed PcdhgC3 led to differences in the tight junction protein expression and mRNA expression of Wnt/mTOR (mechanistic target of rapamycin) pathway genes as well as lower transendothelial electrical resistance. Staining of PcdhgC3 showed diffused cytoplasmic localization in mouse BMEC. Our results suggest that Pcdhs may play a critical role in the barrier-stabilizing pathways at the blood-brain barrier.
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Affiliation(s)
- Christina Dilling
- University of Würzburg, Department of Anaesthesia and Critical Care, Würzburg, Germany
| | - Norbert Roewer
- University of Würzburg, Department of Anaesthesia and Critical Care, Würzburg, Germany
| | - Carola Y Förster
- University of Würzburg, Department of Anaesthesia and Critical Care, Würzburg, Germany
| | - Malgorzata Burek
- University of Würzburg, Department of Anaesthesia and Critical Care, Würzburg, Germany
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31
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Mah KM, Weiner JA. Regulation of Wnt signaling by protocadherins. Semin Cell Dev Biol 2017; 69:158-171. [PMID: 28774578 PMCID: PMC5586504 DOI: 10.1016/j.semcdb.2017.07.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/21/2017] [Accepted: 07/28/2017] [Indexed: 12/23/2022]
Abstract
The ∼70 protocadherins comprise the largest group within the cadherin superfamily. Their diversity, the complexity of the mechanisms through which their genes are regulated, and their many critical functions in nervous system development have engendered a growing interest in elucidating the intracellular signaling pathways through which they act. Recently, multiple protocadherins across several subfamilies have been implicated as modulators of Wnt signaling pathways, and through this as potential tumor suppressors. Here, we review the extant data on the regulation by protocadherins of Wnt signaling pathways and components, and highlight some key unanswered questions that could shape future research.
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Affiliation(s)
- Kar Men Mah
- Department of Biology, The University of Iowa, Iowa City, IA, USA.
| | - Joshua A Weiner
- Department of Biology, The University of Iowa, Iowa City, IA, USA; Department of Psychiatry, The University of Iowa, Iowa City, IA, USA; Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, USA.
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32
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Epigenetic dysregulation of protocadherins in human disease. Semin Cell Dev Biol 2017; 69:172-182. [PMID: 28694114 DOI: 10.1016/j.semcdb.2017.07.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/12/2022]
Abstract
Protocadherins (Pcdhs) are a group of cell-cell adhesion molecules that are highly expressed in the nervous system and have a major function in dendrite development and neural circuit formation. However, the role protocadherins play in human health and disease remains unclear. Several recent studies have associated epigenetic dysregulation of protocadherins with possible implications for disease pathogenesis. In this review, we briefly recap the various epigenetic mechanisms regulating protocadherin genes, particularly the clustered Pcdhs. We further outline research describing altered epigenetic regulation of protocadherins in neurological and psychiatric disorders, as well as in cancer and during aging. We additionally present preliminary data on DNA methylation dynamics of clustered protocadherins during fetal brain development, as well as the epigenetic differences distinguishing adult neuronal and glial cells. A deeper understanding of the role of protocadherins in disease is crucial for designing novel diagnostic tools and therapies targeting brain disorders.
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33
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Bahrami A, Joodi M, Maftooh M, Ferns GA, M. Ahmadi M, Hassanian SM, Avan A. The genetic factors contributing to the development of Wilm's tumor and their clinical utility in its diagnosis and prognosis. J Cell Physiol 2017; 233:2882-2888. [DOI: 10.1002/jcp.26021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/19/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Afsane Bahrami
- Department of Modern Sciences and Technologies; Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
- Student Research Committee; Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
| | - Marjan Joodi
- Department of Pediatric Surgery; Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
- Endoscopic and Minimally Invasive Surgery Research Center; Sarvar Children's Hospital; Mashhad Iran
| | - Mina Maftooh
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
| | - Gordon A. Ferns
- Division of Medical Education, Falmer, Brighton; Brighton and Sussex Medical School; Sussex UK
| | - Mehrdad M. Ahmadi
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
| | - Seyed M. Hassanian
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
| | - Amir Avan
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
- Cancer Research Center; Mashhad University of Medical Sciences; Mashhad Iran
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Laufer BI, Chater-Diehl EJ, Kapalanga J, Singh SM. Long-term alterations to DNA methylation as a biomarker of prenatal alcohol exposure: From mouse models to human children with fetal alcohol spectrum disorders. Alcohol 2017; 60:67-75. [PMID: 28187949 DOI: 10.1016/j.alcohol.2016.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/19/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
Abstract
Rodent models of Fetal Alcohol Spectrum Disorders (FASD) have revealed that prenatal alcohol exposure (PAE) results in differential DNA cytosine methylation in the developing brain. The resulting genome-wide methylation changes are enriched in genes with neurodevelopmental functions. The profile of differential methylation is dynamic and present in some form for life. The methylation changes are transmitted across subsequent mitotic divisions, where they are maintained and further modified over time. More recent follow up has identified a profile of the differential methylation in the buccal swabs of young children born with FASD. While distinct from the profile observed in brain tissue from rodent models, there are similarities. These include changes in genes belonging to a number of neurodevelopmental and behavioral pathways. Specifically, there is increased methylation at the clustered protocadherin genes and deregulation of genomically imprinted genes, even though no single gene is affected in all patients studied to date. These novel results suggest further development of a methylation based strategy could enable early and accurate diagnostics and therapeutics, which have remained a challenge in FASD research. There are two aspects of this challenge that must be addressed in the immediate future: First, the long-term differential methylomics observed in rodent models must be functionally confirmed. Second, the similarities in differential methylation must be further established in humans at a methylomic level and overcome a number of technical limitations. While a cure for FASD is challenging, there is an opportunity for the development of early diagnostics and attenuations towards a higher quality of life.
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Achinger-Kawecka J, Taberlay PC, Clark SJ. Alterations in Three-Dimensional Organization of the Cancer Genome and Epigenome. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 81:41-51. [PMID: 28424341 DOI: 10.1101/sqb.2016.81.031013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The structural and functional basis of the genome is provided by the three-dimensional (3D) chromatin state. To enable accurate gene regulation, enhancer elements and promoter regions are brought into close spatial proximity to ensure proper, cell type-specific gene expression. In cancer, genetic and epigenetic processes can deregulate the transcriptional program. To investigate whether the 3D chromatin state is also disrupted in cancer we performed Hi-C chromosome conformation sequencing in normal and prostate cancer cells and compared the chromatin interaction maps with changes to the genome and epigenome. Notably, we find that additional topologically associated domain (TAD) boundaries are formed in cancer cells resulting in smaller TADs and altered gene expression profiles. The new TAD boundaries are commonly associated with copy-number changes observed in the cancer genome. We also identified new cancer-specific chromatin loops within TADs that are enriched for enhancers and promoters. Finally, we find that many of the long-range epigenetically silenced (LRES) and long-range epigenetically active (LREA) regions in cancer are characterized by differential chromatin interactions. Together our data provide a new insight into charting alterations in higher-order structure and the relationship with genetic, epigenetic, and transcriptional changes across the cancer genome.
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Affiliation(s)
- Joanna Achinger-Kawecka
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia
| | - Phillippa C Taberlay
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia.,School of Medicine, Faculty of Health, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia
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36
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Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma. Neoplasia 2017; 19:100-111. [PMID: 28088687 PMCID: PMC5237802 DOI: 10.1016/j.neo.2016.12.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 02/08/2023] Open
Abstract
Uterine carcinosarcoma (UCS) is a form of endometrial cancer simultaneously exhibiting carcinomatous and sarcomatous elements, but the underlying molecular and epigenetic basis of this disease is poorly understood. We generated complete DNA methylomes for both the carcinomatous and the sarcomatous components of three UCS samples separated by laser capture microdissection and compared DNA methylomes of UCS with those of normal endometrium as well as methylomes derived from endometrioid carcinoma, serous endometrial carcinoma, and endometrial stromal sarcoma. We identified epigenetic lesions specific to carcinosarcoma and specific to its two components. Hallmarks of DNA methylation abnormalities in UCS included global hypomethylation, especially in repetitive elements, and hypermethylation of tumor suppressor gene promoters. Among these, aberrant DNA methylation of MIR200 genes is a key feature of UCS. The carcinoma component of UCS was characterized by hypermethylation of promoters of EMILIN1, NEFM, and CLEC14A, genes that are associated with tumor vascularization. In contrast, DNA methylation changes of PKP3, FAM83F, and TCP11 were more characteristic of the sarcoma components. Our findings highlight the epigenetic signatures that distinguish the two components of UCS, providing a valuable resource for investigation of this disease.
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Abstract
microRNAs (miRNAs) and DNA methylation are the 2 epigenetic modifications that have emerged in recent years as the most critical players in the regulation of gene expression. Compelling evidence has indicated the roles of miRNAs and DNA methylation in modulating cellular transformation and tumorigenesis. miRNAs act as negative regulators of gene expression and are involved in the regulation of both physiologic conditions and during diseases, such as cancer, inflammatory diseases, and psychiatric disorders, among others. Meanwhile, aberrant DNA methylation manifests in both global genome changes and in localized gene promoter changes, which influences the transcription of cancer genes. In this review, we described the mutual regulation of miRNAs and DNA methylation in human cancers. miRNAs regulate DNA methylation by targeting DNA methyltransferases or methylation-related proteins. On the other hand, both hyper- and hypo-methylation of miRNAs occur frequently in human cancers and represent a new level of complexity in gene regulation. Therefore, understanding the mechanisms underlying the mutual regulation of miRNAs and DNA methylation may provide helpful insights in the development of efficient therapeutic approaches.
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Affiliation(s)
- Sumei Wang
- a Department of Oncology , Guangdong Provincial Hospital of Chinese Medicine , Guangzhou, Guangdong , P. R. China.,b Department of Systems Biology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Wanyin Wu
- a Department of Oncology , Guangdong Provincial Hospital of Chinese Medicine , Guangzhou, Guangdong , P. R. China
| | - Francois X Claret
- b Department of Systems Biology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA.,c Experimental Therapeutics Academic Program and Cancer Biology Program , The University of Texas Graduate School of Biomedical Sciences at Houston , Houston , TX , USA
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Abstract
Recent advances in chromosome conformation capture technologies are improving the current appreciation of how 3D genome architecture affects its function in different cell types and disease. Long-range chromatin interactions are organized into topologically associated domains, which are known to play a role in constraining gene expression patterns. However, in cancer cells there are alterations in the 3D genome structure, which impacts on gene regulation. Disruption of topologically associated domains architecture can result in alterations in chromatin interactions that bring new regulatory elements and genes together, leading to altered expression of oncogenes and tumor suppressor genes. Here, we discuss the impact of genetic and epigenetic changes in cancer and how this affects the spatial organization of chromatin. Understanding how disruptions to the 3D architecture contribute to the cancer genome will provide novel insights into the principles of epigenetic gene regulation in cancer and mechanisms responsible for cancer associated mutations and rearrangements.
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Affiliation(s)
- Joanna Achinger-Kawecka
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW 2010, Australia
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39
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Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling. Proc Natl Acad Sci U S A 2016; 113:E8267-E8276. [PMID: 27930333 DOI: 10.1073/pnas.1617802113] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
TET-family dioxygenases catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and oxidized methylcytosines in DNA. Here, we show that mouse embryonic stem cells (mESCs), either lacking Tet3 alone or with triple deficiency of Tet1/2/3, displayed impaired adoption of neural cell fate and concomitantly skewed toward cardiac mesodermal fate. Conversely, ectopic expression of Tet3 enhanced neural differentiation and limited cardiac mesoderm specification. Genome-wide analyses showed that Tet3 mediates cell-fate decisions by inhibiting Wnt signaling, partly through promoter demethylation and transcriptional activation of the Wnt inhibitor secreted frizzled-related protein 4 (Sfrp4). Tet1/2/3-deficient embryos (embryonic day 8.0-8.5) showed hyperactivated Wnt signaling, as well as aberrant differentiation of bipotent neuromesodermal progenitors (NMPs) into mesoderm at the expense of neuroectoderm. Our data demonstrate a key role for TET proteins in modulating Wnt signaling and establishing the proper balance between neural and mesodermal cell fate determination in mouse embryos and ESCs.
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Charlet J, Tomari A, Dallosso AR, Szemes M, Kaselova M, Curry TJ, Almutairi B, Etchevers HC, McConville C, Malik KTA, Brown KW. Genome-wide DNA methylation analysis identifies MEGF10 as a novel epigenetically repressed candidate tumor suppressor gene in neuroblastoma. Mol Carcinog 2016; 56:1290-1301. [PMID: 27862318 PMCID: PMC5396313 DOI: 10.1002/mc.22591] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/03/2016] [Accepted: 11/11/2016] [Indexed: 01/07/2023]
Abstract
Neuroblastoma is a childhood cancer in which many children still have poor outcomes, emphasising the need to better understand its pathogenesis. Despite recent genome‐wide mutation analyses, many primary neuroblastomas do not contain recognizable driver mutations, implicating alternate molecular pathologies such as epigenetic alterations. To discover genes that become epigenetically deregulated during neuroblastoma tumorigenesis, we took the novel approach of comparing neuroblastomas to neural crest precursor cells, using genome‐wide DNA methylation analysis. We identified 93 genes that were significantly differentially methylated of which 26 (28%) were hypermethylated and 67 (72%) were hypomethylated. Concentrating on hypermethylated genes to identify candidate tumor suppressor loci, we found the cell engulfment and adhesion factor gene MEGF10 to be epigenetically repressed by DNA hypermethylation or by H3K27/K9 methylation in neuroblastoma cell lines. MEGF10 showed significantly down‐regulated expression in neuroblastoma tumor samples; furthermore patients with the lowest‐expressing tumors had reduced relapse‐free survival. Our functional studies showed that knock‐down of MEGF10 expression in neuroblastoma cell lines promoted cell growth, consistent with MEGF10 acting as a clinically relevant, epigenetically deregulated neuroblastoma tumor suppressor gene. © 2016 The Authors. Molecular Carcinogenesis Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Jessica Charlet
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Ayumi Tomari
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Anthony R Dallosso
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Marianna Szemes
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Martina Kaselova
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Thomas J Curry
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Bader Almutairi
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Heather C Etchevers
- Faculté de Médecine, Aix-Marseille University, GMGF, UMR_S910, Marseille, France.,Faculté de Médecine, INSERM U910, Marseille, France
| | - Carmel McConville
- Institute of Cancer & Genomic Sciences, University of Birmingham, UK
| | - Karim T A Malik
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Keith W Brown
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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41
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Vieira GC, Chockalingam S, Melegh Z, Greenhough A, Malik S, Szemes M, Park JH, Kaidi A, Zhou L, Catchpoole D, Morgan R, Bates DO, Gabb PD, Malik K. LGR5 regulates pro-survival MEK/ERK and proliferative Wnt/β-catenin signalling in neuroblastoma. Oncotarget 2016; 6:40053-67. [PMID: 26517508 PMCID: PMC4741879 DOI: 10.18632/oncotarget.5548] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/19/2015] [Indexed: 12/14/2022] Open
Abstract
LGR5 is a marker of normal and cancer stem cells in various tissues where it functions as a receptor for R-spondins and increases canonical Wnt signalling amplitude. Here we report that LGR5 is also highly expressed in a subset of high grade neuroblastomas. Neuroblastoma is a clinically heterogenous paediatric cancer comprising a high proportion of poor prognosis cases (~40%) which are frequently lethal. Unlike many cancers, Wnt pathway mutations are not apparent in neuroblastoma, although previous microarray analyses have implicated deregulated Wnt signalling in high-risk neuroblastoma. We demonstrate that LGR5 facilitates high Wnt signalling in neuroblastoma cell lines treated with Wnt3a and R-spondins, with SK-N-BE(2)-C, SK-N-NAS and SH-SY5Y cell-lines all displaying strong Wnt induction. These lines represent MYCN-amplified, NRAS and ALK mutant neuroblastoma subtypes respectively. Wnt3a/R-Spondin treatment also promoted nuclear translocation of β-catenin, increased proliferation and activation of Wnt target genes. Strikingly, short-interfering RNA mediated knockdown of LGR5 induces dramatic Wnt-independent apoptosis in all three cell-lines, accompanied by greatly diminished phosphorylation of mitogen/extracellular signal-regulated kinases (MEK1/2) and extracellular signal-regulated kinases (ERK1/2), and an increase of BimEL, an apoptosis facilitator downstream of ERK. Akt signalling is also decreased by a Rictor dependent, PDK1-independent mechanism. LGR5 expression is cell cycle regulated and LGR5 depletion triggers G1 cell-cycle arrest, increased p27 and decreased phosphorylated retinoblastoma protein. Our study therefore characterises new cancer-associated pathways regulated by LGR5, and suggest that targeting of LGR5 may be of therapeutic benefit for neuroblastomas with diverse etiologies, as well as other cancers expressing high LGR5.
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Affiliation(s)
- Gabriella Cunha Vieira
- Cancer Epigenetics Laboratory and School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - S Chockalingam
- Cancer Epigenetics Laboratory and School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Zsombor Melegh
- Department of Cellular Pathology, Southmead Hospital, Bristol, UK
| | - Alexander Greenhough
- Colorectal Cancer Laboratory, School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Sally Malik
- Cancer Epigenetics Laboratory and School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Marianna Szemes
- Cancer Epigenetics Laboratory and School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Ji Hyun Park
- Cancer Epigenetics Laboratory and School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Abderrahmane Kaidi
- Cancer Epigenetics Laboratory and School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Li Zhou
- The Kids Research Institute, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Daniel Catchpoole
- The Kids Research Institute, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Rhys Morgan
- Colorectal Cancer Laboratory, School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - David O Bates
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Peter David Gabb
- Cancer Epigenetics Laboratory and School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Karim Malik
- Cancer Epigenetics Laboratory and School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
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42
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Mah KM, Houston DW, Weiner JA. The γ-Protocadherin-C3 isoform inhibits canonical Wnt signalling by binding to and stabilizing Axin1 at the membrane. Sci Rep 2016; 6:31665. [PMID: 27530555 PMCID: PMC4987702 DOI: 10.1038/srep31665] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/21/2016] [Indexed: 01/14/2023] Open
Abstract
The 22 γ-Protocadherin (γ-Pcdh) adhesion molecules encoded by the Pcdhg gene cluster play critical roles in nervous system development, including regulation of dendrite arborisation, neuronal survival, and synaptogenesis. Recently, they have been implicated in suppression of tumour cell growth by inhibition of canonical Wnt signalling, though the mechanisms through which this occurs remain unknown. Here, we show differential regulation of Wnt signalling by individual γ-Pcdhs: The C3 isoform uniquely inhibits the pathway, whilst 13 other isoforms upregulate signalling. Focusing on the C3 isoform, we show that its unique variable cytoplasmic domain (VCD) is the critical one for Wnt pathway inhibition. γ-Pcdh-C3, but not other isoforms, physically interacts with Axin1, a key component of the canonical Wnt pathway. The C3 VCD competes with Dishevelled for binding to the DIX domain of Axin1, which stabilizes Axin1 at the membrane and leads to reduced phosphorylation of Wnt co-receptor Lrp6. Finally, we present evidence that Wnt pathway activity can be modulated up (by γ-Pcdh-A1) or down (by γ-Pcdh-C3) in the cerebral cortex in vivo, using conditional transgenic alleles. Together, these data delineate opposing roles for γ-Pcdh isoforms in regulating Wnt signalling and identify Axin1 as a novel protein interactor of the widely-expressed γ-Pcdh-C3 isoform.
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Affiliation(s)
- Kar Men Mah
- Department of Biology, The University of Iowa, 143 Biology Building, Iowa City, 52242, IA, USA.,Integrated Biology Graduate Program, The University of Iowa, 143 Biology Building, Iowa City,52242, IA, USA
| | - Douglas W Houston
- Department of Biology, The University of Iowa, 143 Biology Building, Iowa City, 52242, IA, USA
| | - Joshua A Weiner
- Department of Biology, The University of Iowa, 143 Biology Building, Iowa City, 52242, IA, USA.,Department of Psychiatry, University of Iowa Carver College of Medicine, 200 Hawkins Drive, Iowa City, 52242, IA, USA
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43
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Shan M, Su Y, Kang W, Gao R, Li X, Zhang G. Aberrant expression and functions of protocadherins in human malignant tumors. Tumour Biol 2016; 37:12969-12981. [PMID: 27449047 DOI: 10.1007/s13277-016-5169-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 07/12/2016] [Indexed: 12/11/2022] Open
Abstract
Protocadherins (PCDHs) are a group of transmembrane proteins belonging to the cadherin superfamily and are subdivided into "clustered" and "non-clustered" groups. PCDHs vary in both structure and interaction partners and thus regulate multiple biological responses in complex and versatile patterns. Previous researches showed that PCDHs regulated the development of brain and were involved in some neuronal diseases. Recently, studies have revealed aberrant expression of PCDHs in various human malignant tumors. The down-regulation or absence of PCDHs in malignant cells has been associated with cancer progression. Further researches suggest that PCDHs may play major functions as tumor suppressor by inhibiting the proliferation and metastasis of cancer cells. In this review, we focus on the altered expression of PCDHs and their roles in the development of cancer progression. We also discuss the potential mechanisms, by which PCDHs are aberrantly expressed, and its implications in regulating cancers.
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Affiliation(s)
- Ming Shan
- Department of Breast Surgery, the Affiliated Tumor Hospital of Harbin Medical University, Harbin, China
| | - Yonghui Su
- Department of Breast Surgery, the Affiliated Tumor Hospital of Harbin Medical University, Harbin, China
| | - Wenli Kang
- Department of Oncology, General Hospital of Hei Longjiang Province Land Reclamation Headquarter, Harbin, China
| | - Ruixin Gao
- Department of Breast Surgery, The First Hospital of Qiqihaer City, Qiqihaer, China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, China.
| | - Guoqiang Zhang
- Department of Breast Surgery, the Affiliated Tumor Hospital of Harbin Medical University, Harbin, China.
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44
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de Freitas GB, Gonçalves RA, Gralle M. Functional test of PCDHB11, the most human-specific neuronal surface protein. BMC Evol Biol 2016; 16:75. [PMID: 27068704 PMCID: PMC4828864 DOI: 10.1186/s12862-016-0652-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/06/2016] [Indexed: 12/04/2022] Open
Abstract
Background Brain-expressed proteins that have undergone functional change during human evolution may contribute to human cognitive capacities, and may also leave us vulnerable to specifically human diseases, such as schizophrenia, autism or Alzheimer’s disease. In order to search systematically for those proteins that have changed the most during human evolution and that might contribute to brain function and pathology, all proteins with orthologs in chimpanzee, orangutan and rhesus macaque and annotated as being expressed on the surface of cells in the human central nervous system were ordered by the number of human-specific amino acid differences that are fixed in modern populations. Results PCDHB11, a beta-protocadherin homologous to murine cell adhesion proteins, stood out with 12 substitutions and maintained its lead after normalizing for protein size and applying weights for amino acid exchange probabilities. Human PCDHB11 was found to cause homophilic cell adhesion, but at lower levels than shown for other clustered protocadherins. Homophilic adhesion caused by a PCDHB11 with reversion of human-specific changes was as low as for modern human PCDHB11; while neither human nor reverted PCDHB11 adhered to controls, they did adhere to each other. A loss of function in PCDHB11 is unlikely because intra-human variability did not increase relative to the other human beta-protocadherins. Conclusions The brain-expressed protein with the highest number of human-specific substitutions is PCDHB11. In spite of its fast evolution and low intra-human variability, cell-based tests on the only proposed function for PCDHB11 did not indicate a functional change.
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Affiliation(s)
- Guilherme Braga de Freitas
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafaella Araújo Gonçalves
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matthias Gralle
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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45
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Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Res 2016; 26:719-31. [PMID: 27053337 PMCID: PMC4889976 DOI: 10.1101/gr.201517.115] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/04/2016] [Indexed: 12/29/2022]
Abstract
A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type–specific gene expression profiles. Here, we performed Hi-C chromosome conformation capture sequencing to investigate how three-dimensional chromatin organization is disrupted in the context of copy-number variation, long-range epigenetic remodeling, and atypical gene expression programs in prostate cancer. We find that cancer cells retain the ability to segment their genomes into megabase-sized topologically associated domains (TADs); however, these domains are generally smaller due to establishment of additional domain boundaries. Interestingly, a large proportion of the new cancer-specific domain boundaries occur at regions that display copy-number variation. Notably, a common deletion on 17p13.1 in prostate cancer spanning the TP53 tumor suppressor locus results in bifurcation of a single TAD into two distinct smaller TADs. Change in domain structure is also accompanied by novel cancer-specific chromatin interactions within the TADs that are enriched at regulatory elements such as enhancers, promoters, and insulators, and associated with alterations in gene expression. We also show that differential chromatin interactions across regulatory regions occur within long-range epigenetically activated or silenced regions of concordant gene activation or repression in prostate cancer. Finally, we present a novel visualization tool that enables integrated exploration of Hi-C interaction data, the transcriptome, and epigenome. This study provides new insights into the relationship between long-range epigenetic and genomic dysregulation and changes in higher-order chromatin interactions in cancer.
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46
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Timofeeva MN, Kinnersley B, Farrington SM, Whiffin N, Palles C, Svinti V, Lloyd A, Gorman M, Ooi LY, Hosking F, Barclay E, Zgaga L, Dobbins S, Martin L, Theodoratou E, Broderick P, Tenesa A, Smillie C, Grimes G, Hayward C, Campbell A, Porteous D, Deary IJ, Harris SE, Northwood EL, Barrett JH, Smith G, Wolf R, Forman D, Morreau H, Ruano D, Tops C, Wijnen J, Schrumpf M, Boot A, Vasen HFA, Hes FJ, van Wezel T, Franke A, Lieb W, Schafmayer C, Hampe J, Buch S, Propping P, Hemminki K, Försti A, Westers H, Hofstra R, Pinheiro M, Pinto C, Teixeira M, Ruiz-Ponte C, Fernández-Rozadilla C, Carracedo A, Castells A, Castellví-Bel S, Campbell H, Bishop DT, Tomlinson IPM, Dunlop MG, Houlston RS. Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer. Sci Rep 2015; 5:16286. [PMID: 26553438 PMCID: PMC4639776 DOI: 10.1038/srep16286] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/21/2015] [Indexed: 12/21/2022] Open
Abstract
Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and 29,045 controls from six European populations. Single-variant analysis identified a coding variant (rs3184504) in SH2B3 (12q24) associated with CRC risk (OR = 1.08, P = 3.9 × 10(-7)), and novel damaging coding variants in 3 genes previously tagged by GWAS efforts; rs16888728 (8q24) in UTP23 (OR = 1.15, P = 1.4 × 10(-7)); rs6580742 and rs12303082 (12q13) in FAM186A (OR = 1.11, P = 1.2 × 10(-7) and OR = 1.09, P = 7.4 × 10(-8)); rs1129406 (12q13) in ATF1 (OR = 1.11, P = 8.3 × 10(-9)), all reaching exome-wide significance levels. Gene based tests identified associations between CRC and PCDHGA genes (P < 2.90 × 10(-6)). We found an excess of rare, damaging variants in base-excision (P = 2.4 × 10(-4)) and DNA mismatch repair genes (P = 6.1 × 10(-4)) consistent with a recessive mode of inheritance. This study comprehensively explores the contribution of coding sequence variation to CRC risk, identifying associations with coding variation in 4 genes and PCDHG gene cluster and several candidate recessive alleles. However, these findings suggest that recurrent, low-frequency coding variants account for a minority of the unexplained heritability of CRC.
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Affiliation(s)
- Maria N. Timofeeva
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Susan M. Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Victoria Svinti
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Amy Lloyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Maggie Gorman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Li-Yin Ooi
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Fay Hosking
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Lina Zgaga
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Sara Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Evropi Theodoratou
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, United Kingdom
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Roslin EH25 9RG, United Kingdom
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Claire Smillie
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Graeme Grimes
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Archie Campbell
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Generation Scotland, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - David Porteous
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Generation Scotland, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Ian J. Deary
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, United Kingdom
| | - Sarah E. Harris
- Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, United Kingdom
| | - Emma L. Northwood
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Jennifer H. Barrett
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Gillian Smith
- Medical Research Institute, University of Dundee, Dundee, UK
| | - Roland Wolf
- Medical Research Institute, University of Dundee, Dundee, UK
| | | | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Carli Tops
- Department of Clinical Genetics, Leiden University Medical Center, The Netherlands
| | - Juul Wijnen
- Department of Human Genetics, Leiden University Medical Center, The Netherlands
| | - Melanie Schrumpf
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Hans F A Vasen
- Department of Gastroenterology, Leiden University Medical Center, The Netherlands
| | - Frederik J. Hes
- Department of Clinical Genetics, Leiden University Medical Center, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, The Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wolgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University Kiel, Kiel
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Stephan Buch
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden, Germany
| | - Peter Propping
- Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 205 02 Malmö, Sweden
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, 205 02 Malmö, Sweden
| | - Helga Westers
- University of Groningen, University Medical Centre Groningen, Department of Genetics, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Robert Hofstra
- University of Groningen, University Medical Centre Groningen, Department of Genetics, PO Box 30001, 9700 RB Groningen, the Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, the Netherlands
| | - Manuela Pinheiro
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Manuel Teixeira
- Department of Genetics, Portuguese Oncology Institute and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, 15706 Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Ceres Fernández-Rozadilla
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, 15706 Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Angel Carracedo
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, 15706 Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Antoni Castells
- Servei de Gastroenterologia, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Servei de Gastroenterologia, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Harry Campbell
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, United Kingdom
| | - D. Timothy Bishop
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Ian P M Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
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Strong E, Butcher D, Singhania R, Mervis C, Morris C, De Carvalho D, Weksberg R, Osborne L. Symmetrical Dose-Dependent DNA-Methylation Profiles in Children with Deletion or Duplication of 7q11.23. Am J Hum Genet 2015; 97:216-27. [PMID: 26166478 DOI: 10.1016/j.ajhg.2015.05.019] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022] Open
Abstract
Epigenetic dysfunction has been implicated in a growing list of disorders that include cancer, neurodevelopmental disorders, and neurodegeneration. Williams syndrome (WS) and 7q11.23 duplication syndrome (Dup7) are rare neurodevelopmental disorders with broad phenotypic spectra caused by deletion and duplication, respectively, of a 1.5-Mb region that includes several genes with a role in epigenetic regulation. We have identified striking differences in DNA methylation across the genome between blood cells from children with WS or Dup7 and blood cells from typically developing (TD) children. Notably, regions that were differentially methylated in both WS and Dup7 displayed a significant and symmetrical gene-dose-dependent effect, such that WS typically showed increased and Dup7 showed decreased DNA methylation. Differentially methylated genes were significantly enriched with genes in pathways involved in neurodevelopment, autism spectrum disorder (ASD) candidate genes, and imprinted genes. Using alignment with ENCODE data, we also found the differentially methylated regions to be enriched with CCCTC-binding factor (CTCF) binding sites. These findings suggest that gene(s) within 7q11.23 alter DNA methylation at specific sites across the genome and result in dose-dependent DNA-methylation profiles in WS and Dup7. Given the extent of DNA-methylation changes and the potential impact on CTCF binding and chromatin regulation, epigenetic mechanisms most likely contribute to the complex neurological phenotypes of WS and Dup7. Our findings highlight the importance of DNA methylation in the pathogenesis of WS and Dup7 and provide molecular mechanisms that are potentially shared by WS, Dup7, and ASD.
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Rafique S, Thomas JS, Sproul D, Bickmore WA. Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer. Genome Biol 2015; 16:145. [PMID: 26235388 PMCID: PMC4536608 DOI: 10.1186/s13059-015-0719-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/06/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to identify large chromosomal domains of epigenetic dysregulation in breast cancers. RESULTS We identify large regions of coordinate down-regulation of gene expression, and other regions of coordinate activation, in breast cancers and show that these regions are linked to tumor subtype. In particular we show that a group of coordinately regulated regions are expressed in luminal, estrogen-receptor positive breast tumors and cell lines. For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus. In MCF7 cells, we show that this depends on the presence of estrogen. CONCLUSIONS Our data suggest that the liganded estrogen receptor is linked to long-range changes in higher-order chromatin organization and epigenetic dysregulation in cancer. This may suggest that as well as drugs targeting histone modifications, it will be valuable to investigate the inhibition of protein complexes involved in chromatin folding in cancer cells.
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Affiliation(s)
- Sehrish Rafique
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. .,Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Jeremy S Thomas
- Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. .,Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
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PCDH10 inhibits cell proliferation of multiple myeloma via the negative regulation of the Wnt/β-catenin/BCL-9 signaling pathway. Oncol Rep 2015; 34:747-54. [PMID: 26081897 DOI: 10.3892/or.2015.4056] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/04/2015] [Indexed: 11/05/2022] Open
Abstract
The tumor suppressor protocadherin-10 (PCDH10) gene is important in cell proliferation, survival, apoptosis and migration. Inactivation of PCDH10 by promoter methylation is a frequent pathogenetic event in multiple myeloma (MM). The Wnt/β-catenin pathway is known to be involved in the cell growth of various types of cancer, including MM. However, the relationship between PCDH10 and Wnt signaling in MM remains unclear. In this study, we found that PCDH10 deficiency highly enhanced MM cell proliferation, Wnt signaling and the expression of BCL-9, an essential coactivator of Wnt transcriptional activity that is correlated with cell growth, survival and drug resistance. Restoration of PCDH10 suppressed nuclear localization of β-catenin, the activity of LEF/TCF, the expression of BCL-9 and AKT, whereas the expression of GSK3β was increased. The antagonistic effect of PCDH10 was associated with G1-phase blockage. Collectively, PCDH10 antagonized MM cell proliferation via the downregulation of Wnt/β-catenin/BCL-9 signaling, whereas PCDH10 repressed the expression of AKT to promote the expression of GSK3β and then to restrain the activation of β-catenin. Thus, the results offer a novel preclinical rationale in order to explore PCDH10 as an effective and selective therapeutic strategy to eradicate MM cells.
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50
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de Matos Simoes R, Dalleau S, Williamson KE, Emmert-Streib F. Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. BMC SYSTEMS BIOLOGY 2015; 9:21. [PMID: 25971253 PMCID: PMC4460634 DOI: 10.1186/s12918-015-0165-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 04/22/2015] [Indexed: 12/18/2022]
Abstract
BACKGROUND Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is crucial in order to improve our current limited understanding of urothelial cancer (UC) on the molecular level. The inference of genome-wide gene regulatory networks (GRN) from large-scale gene expression data provides a promising approach for a detailed investigation of the underlying network structure associated to urothelial carcinogenesis. METHODS In our study we inferred and compared three GRNs by the application of the BC3Net inference algorithm to large-scale transitional cell carcinoma gene expression data sets from Illumina RNAseq (179 samples), Illumina Bead arrays (165 samples) and Affymetrix Oligo microarrays (188 samples). We investigated the structural and functional properties of GRNs for the identification of molecular targets associated to urothelial cancer. RESULTS We found that the urothelial cancer (UC) GRNs show a significant enrichment of subnetworks that are associated with known cancer hallmarks including cell cycle, immune response, signaling, differentiation and translation. Interestingly, the most prominent subnetworks of co-located genes were found on chromosome regions 5q31.3 (RNAseq), 8q24.3 (Oligo) and 1q23.3 (Bead), which all represent known genomic regions frequently deregulated or aberated in urothelial cancer and other cancer types. Furthermore, the identified hub genes of the individual GRNs, e.g., HID1/DMC1 (tumor development), RNF17/TDRD4 (cancer antigen) and CYP4A11 (angiogenesis/ metastasis) are known cancer associated markers. The GRNs were highly dataset specific on the interaction level between individual genes, but showed large similarities on the biological function level represented by subnetworks. Remarkably, the RNAseq UC GRN showed twice the proportion of significant functional subnetworks. Based on our analysis of inferential and experimental networks the Bead UC GRN showed the lowest performance compared to the RNAseq and Oligo UC GRNs. CONCLUSION To our knowledge, this is the first study investigating genome-scale UC GRNs. RNAseq based gene expression data is the data platform of choice for a GRN inference. Our study offers new avenues for the identification of novel putative diagnostic targets for subsequent studies in bladder tumors.
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Affiliation(s)
- Ricardo de Matos Simoes
- Centre for Cancer Research and Cell Biology (CCRCB), Queens University Belfast, 97 Lisburn Road, Belfast, County Antrim, Northern Ireland, UK.
| | - Sabine Dalleau
- Centre for Cancer Research and Cell Biology (CCRCB), Queens University Belfast, 97 Lisburn Road, Belfast, County Antrim, Northern Ireland, UK.
| | - Kate E Williamson
- Centre for Cancer Research and Cell Biology (CCRCB), Queens University Belfast, 97 Lisburn Road, Belfast, County Antrim, Northern Ireland, UK.
| | - Frank Emmert-Streib
- Computational Medicine and Statistical Learning Laboratory, Department of Signal Processing, Tampere University of Technology, Tampere, 33720, Finland. .,Institute of Biosciences and Medical Technology, Tampere, 33520, Finland.
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