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Visone R, Bacalini MG, Di Franco S, Ferracin M, Colorito ML, Pagotto S, Laprovitera N, Licastro D, Di Marco M, Scavo E, Bassi C, Saccenti E, Nicotra A, Grzes M, Garagnani P, De Laurenzi V, Valeri N, Mariani-Costantini R, Negrini M, Stassi G, Veronese A. DNA methylation of shelf, shore and open sea CpG positions distinguish high microsatellite instability from low or stable microsatellite status colon cancer stem cells. Epigenomics 2019; 11:587-604. [PMID: 31066579 DOI: 10.2217/epi-2018-0153] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: To investigate the genome-wide methylation of genetically characterized colorectal cancer stem cell (CR-CSC) lines. Materials & methods: Eight CR-CSC lines were isolated from primary colorectal cancer (CRC) tissues, cultured and characterized for aneuploidy, mutational status of CRC-related genes and microsatellite instability (MSI). Genome-wide DNA methylation was assessed by MethylationEPIC microarray. Results: We describe a distinctive methylation pattern that is maintained following in vivo passages in immune-compromised mice. We identified an epigenetic CR-CSC signature associated with MSI. We noticed that the preponderance of the differentially methylated positions do not reside at CpG islands, but spread to shelf and open sea regions. Conclusion: Given that CRCs with MSI-high status have a lower metastatic potential, the identification of a MSI-related methylation signature could provide new insights and possible targets into metastatic CRC.
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Affiliation(s)
- Rosa Visone
- Department of Medical, Oral & Biotechnological Sciences, G. d'Annunzio University, Chieti-Pescara, Italy
- Center of Aging Science & Translational Medicine (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | | | - Simone Di Franco
- Cellular & Molecular Pathophysiology Laboratory, Department of Surgical, Oncological & Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic & Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Luisa Colorito
- Cellular & Molecular Pathophysiology Laboratory, Department of Surgical, Oncological & Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Sara Pagotto
- Department of Medical, Oral & Biotechnological Sciences, G. d'Annunzio University, Chieti-Pescara, Italy
- Center of Aging Science & Translational Medicine (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | - Noemi Laprovitera
- Department of Experimental, Diagnostic & Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | | | - Mirco Di Marco
- Department of Medical, Oral & Biotechnological Sciences, G. d'Annunzio University, Chieti-Pescara, Italy
- Center of Aging Science & Translational Medicine (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | - Emanuela Scavo
- Department of Experimental, Diagnostic & Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Cristian Bassi
- Department of Morphology, Surgery & Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Elena Saccenti
- Department of Morphology, Surgery & Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Annalisa Nicotra
- Department of Experimental, Diagnostic & Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Grzes
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
- Department of Molecular Biology, Institute of Genetics & Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
| | - Paolo Garagnani
- Department of Experimental, Diagnostic & Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Vincenzo De Laurenzi
- Department of Medical, Oral & Biotechnological Sciences, G. d'Annunzio University, Chieti-Pescara, Italy
- Center of Aging Science & Translational Medicine (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Renato Mariani-Costantini
- Department of Medical, Oral & Biotechnological Sciences, G. d'Annunzio University, Chieti-Pescara, Italy
- Center of Aging Science & Translational Medicine (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | - Massimo Negrini
- Department of Morphology, Surgery & Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Giorgio Stassi
- Department of Experimental, Diagnostic & Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Angelo Veronese
- Center of Aging Science & Translational Medicine (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
- Department of Medicine & Aging Science, G. d'Annunzio University, Chieti-Pescara, Italy
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Laprovitera N, Grzes M, Porcellini E, Ferracin M. Cancer Site-Specific Multiple microRNA Quantification by Droplet Digital PCR. Front Oncol 2018; 8:447. [PMID: 30374423 PMCID: PMC6196277 DOI: 10.3389/fonc.2018.00447] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 08/03/2018] [Accepted: 09/24/2018] [Indexed: 01/04/2023] Open
Abstract
Archival formalin-fixed paraffin-embedded (FFPE) tissues represent an extraordinary source of smallRNAs, including microRNAs (miRNAs). Contrary to other RNA molecules, miRNAs are stable, nuclease-resistant and quantifiable even in low quality samples. The accurate assessment of miRNA levels in archival samples is of great interest for many pathological conditions, including cancer. In human tumors, microRNA expression is type-specific and can be used as diagnostic, prognostic or response-to-treatment biomarker. In this study, we provide a method for multiple miRNA quantification in 96-well plates, using EvaGreen-based droplet digital PCR technology and miRCURY LNA miRNA assays. This approach allows the absolute quantification of a customizable panel of miRNAs at the same time and under identical experimental conditions, to be used for diagnostic or prognostic applications.
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Affiliation(s)
- Noemi Laprovitera
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Grzes
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Department of Molecular Biology, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Lesznowola, Poland
| | - Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
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Cieslak J, Skorczyk A, Stachowiak M, Szydlowski M, Grzes M, Paczynska P, Skowronska B, Majewska K, Stankiewicz W, Fichna P, Switonski M. Polymorphisms in 5′-flanking regions of genes encoding adiponectin, leptin, and resistin are not associated with obesity of Polish children and adolescents. Mol Biol Rep 2010; 38:1793-8. [DOI: 10.1007/s11033-010-0294-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 09/02/2010] [Indexed: 10/19/2022]
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Grzes M, Nowacka-Woszuk J, Szczerbal I, Czerwinska J, Gracz J, Switonski M. A comparison of coding sequence and cytogenetic localization of the myostatin gene in the dog, red fox, arctic fox and Chinese raccoon dog. Cytogenet Genome Res 2009; 126:173-9. [PMID: 20016167 DOI: 10.1159/000245917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2009] [Indexed: 11/19/2022] Open
Abstract
The gene encoding myostatin (MSTN), due to its crucial function for growth of skeletal muscle mass, is an important candidate for muscularity. In this study we analyzed the nucleotide sequence and FISH localization of this gene in 4 canids, including 3 farm species. The nucleotide sequence of the MSTN coding fragment turned out to be highly conserved, since its identity among the studied species was very high and varied between 99.4 and 99.7%. Only 1, widely spread, silent single nucleotide polymorphism (SNP) was found in exon 1 of the Chinese raccoon dog. The MSTN gene was localized close to the centromere in one-armed chromosomes of the dog (37q11) and bi-armed chromosomes of the red fox (16p11) and arctic fox (10q11), with an exception of the Chinese raccoon dog chromosome (2q14-q21). This chromosome is orthologous to 3 canine chromosomes and thus the MSTN was found more interstitially. Our results are in agreement with the hypothesis that karyotypes of the canids evolved mainly through centric fusion/fission events, while tandem fusions occurred rarely.
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Affiliation(s)
- M Grzes
- Poznan University of Life Sciences, Poznan, Poland
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