Genome-wide DNA methylation analysis identifies promoter hypermethylation in canine malignant melanoma

Canine malignant melanoma is a common cancer with a high mortality rate. Although previous studies have evaluated various aspects of this tumour, the exact mechanism of tumourigenesis remains unknown. Epigenetic mechanisms, such as DNA methylation, have recently gained attention as aetiological fact...

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Veröffentlicht in:Research in veterinary science 2020-10, Vol.132, p.521-526
Hauptverfasser: Ishizaki, T., Yamazaki, J., Jelinek, J., Aoshima, K., Kimura, T.
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Yamazaki, J.
Jelinek, J.
Aoshima, K.
Kimura, T.
description Canine malignant melanoma is a common cancer with a high mortality rate. Although previous studies have evaluated various aspects of this tumour, the exact mechanism of tumourigenesis remains unknown. Epigenetic mechanisms, such as DNA methylation, have recently gained attention as aetiological factors for neoplasia in humans. This study aimed to analyse genome-wide DNA methylation patterns in canine malignant melanoma based on next-generation sequencing data. A total of 76,213 CpG sites, including 29,482 sites in CpG islands (CGIs), were analysed using next-generation sequencing of methylation-specific signatures, obtained by sequential digestion with enzymes, to compare normal oral mucosal samples from four healthy dogs, four canine melanoma cell lines (3 oral cavity and 1 skin), and five clinical samples of oral canine melanoma. Malignant melanoma showed increased methylation at thousands of normally unmethylated CpG sites in CGIs and decreased methylation at normally methylated CpG sites in non-CGIs. Interestingly, the promoter regions of 81–393 genes were hypermethylated; 23 of these genes were present in all melanoma cell lines and melanoma clinical samples. Among these 23 genes, six genes with “sequence-specific DNA binding” annotation were significantly enriched, including three Homeobox genes—HMX2, TLX2, and HOXA9—that may be involved in the tumourigenesis of canine malignant melanoma. This study revealed widespread alterations in DNA methylation and a large number of hypermethylated genes in canine malignant melanoma. •Genome-wide DNA methylation pattern of canine malignant melanoma cell lines and clinical cases were analysed.•Genome-wide DNA methylation pattern of canine malignant melanoma was apparently different from that of normal oral tissues.•DNA methylation levels were increased in CpG islands (CGIs) and decreased in non-CGIs (NCGIs) in melanoma.•Hundreds of common hypermethylated genes were identified in malignant melanoma.
doi_str_mv 10.1016/j.rvsc.2020.08.006
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Although previous studies have evaluated various aspects of this tumour, the exact mechanism of tumourigenesis remains unknown. Epigenetic mechanisms, such as DNA methylation, have recently gained attention as aetiological factors for neoplasia in humans. This study aimed to analyse genome-wide DNA methylation patterns in canine malignant melanoma based on next-generation sequencing data. A total of 76,213 CpG sites, including 29,482 sites in CpG islands (CGIs), were analysed using next-generation sequencing of methylation-specific signatures, obtained by sequential digestion with enzymes, to compare normal oral mucosal samples from four healthy dogs, four canine melanoma cell lines (3 oral cavity and 1 skin), and five clinical samples of oral canine melanoma. Malignant melanoma showed increased methylation at thousands of normally unmethylated CpG sites in CGIs and decreased methylation at normally methylated CpG sites in non-CGIs. 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This study revealed widespread alterations in DNA methylation and a large number of hypermethylated genes in canine malignant melanoma. •Genome-wide DNA methylation pattern of canine malignant melanoma cell lines and clinical cases were analysed.•Genome-wide DNA methylation pattern of canine malignant melanoma was apparently different from that of normal oral tissues.•DNA methylation levels were increased in CpG islands (CGIs) and decreased in non-CGIs (NCGIs) in melanoma.•Hundreds of common hypermethylated genes were identified in malignant melanoma.</description><identifier>ISSN: 0034-5288</identifier><identifier>EISSN: 1532-2661</identifier><identifier>DOI: 10.1016/j.rvsc.2020.08.006</identifier><identifier>PMID: 32810831</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Animals ; Annotations ; Biotechnology ; Canine malignant melanoma ; Cell Line, Tumor ; CpG Islands ; Deoxyribonucleic acid ; DNA ; DNA Methylation ; DNA sequencing ; Dog Diseases - genetics ; Dogs ; Enzymes ; Epigenesis, Genetic ; Epigenetics ; Females ; Gene expression ; Genes ; Genome-wide analysis ; Genome-Wide Association Study ; Genomes ; High-Throughput Nucleotide Sequencing - veterinary ; Homeobox ; Melanoma ; Melanoma - genetics ; Melanoma - veterinary ; Mucosa ; Next-generation sequencing ; Nucleotide sequence ; Ontology ; Oral cavity ; Promoter Regions, Genetic ; Skin cancer ; Tlx2 protein ; Tumorigenesis ; Tumors ; Veterinary medicine</subject><ispartof>Research in veterinary science, 2020-10, Vol.132, p.521-526</ispartof><rights>2020 Elsevier Ltd</rights><rights>Copyright © 2020 Elsevier Ltd. 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Although previous studies have evaluated various aspects of this tumour, the exact mechanism of tumourigenesis remains unknown. Epigenetic mechanisms, such as DNA methylation, have recently gained attention as aetiological factors for neoplasia in humans. This study aimed to analyse genome-wide DNA methylation patterns in canine malignant melanoma based on next-generation sequencing data. A total of 76,213 CpG sites, including 29,482 sites in CpG islands (CGIs), were analysed using next-generation sequencing of methylation-specific signatures, obtained by sequential digestion with enzymes, to compare normal oral mucosal samples from four healthy dogs, four canine melanoma cell lines (3 oral cavity and 1 skin), and five clinical samples of oral canine melanoma. Malignant melanoma showed increased methylation at thousands of normally unmethylated CpG sites in CGIs and decreased methylation at normally methylated CpG sites in non-CGIs. 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This study revealed widespread alterations in DNA methylation and a large number of hypermethylated genes in canine malignant melanoma. •Genome-wide DNA methylation pattern of canine malignant melanoma cell lines and clinical cases were analysed.•Genome-wide DNA methylation pattern of canine malignant melanoma was apparently different from that of normal oral tissues.•DNA methylation levels were increased in CpG islands (CGIs) and decreased in non-CGIs (NCGIs) in melanoma.•Hundreds of common hypermethylated genes were identified in malignant melanoma.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>32810831</pmid><doi>10.1016/j.rvsc.2020.08.006</doi><tpages>6</tpages></addata></record>
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source MEDLINE; Elsevier ScienceDirect Journals
subjects Animals
Annotations
Biotechnology
Canine malignant melanoma
Cell Line, Tumor
CpG Islands
Deoxyribonucleic acid
DNA
DNA Methylation
DNA sequencing
Dog Diseases - genetics
Dogs
Enzymes
Epigenesis, Genetic
Epigenetics
Females
Gene expression
Genes
Genome-wide analysis
Genome-Wide Association Study
Genomes
High-Throughput Nucleotide Sequencing - veterinary
Homeobox
Melanoma
Melanoma - genetics
Melanoma - veterinary
Mucosa
Next-generation sequencing
Nucleotide sequence
Ontology
Oral cavity
Promoter Regions, Genetic
Skin cancer
Tlx2 protein
Tumorigenesis
Tumors
Veterinary medicine
title Genome-wide DNA methylation analysis identifies promoter hypermethylation in canine malignant melanoma
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