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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: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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