Copy number rather than epigenetic alterations are the major dictator of imprinted methylation in tumors

Alex Martin-Trujillo, Enrique Vidal, Ana Monteagudo-Sánchez, Marta Sanchez-Delgado, Sebastian Moran, Jose Ramon Hernandez Mora, Holger Heyn, Miriam Guitart, Manel Esteller and David Monk ()
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Alex Martin-Trujillo: Institut d’Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L’Hospitalet de Llobregat
Enrique Vidal: The Barcelona Institute of Science and Technology
Ana Monteagudo-Sánchez: Institut d’Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L’Hospitalet de Llobregat
Marta Sanchez-Delgado: Institut d’Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L’Hospitalet de Llobregat
Sebastian Moran: Institut d’Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L’Hospitalet de Llobregat
Jose Ramon Hernandez Mora: Institut d’Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L’Hospitalet de Llobregat
Holger Heyn: Barcelona, Spain Universitat Pompeu Fabra (UPF)
Miriam Guitart: UDIAT- Diagnostic Centre, Corporació Sanitària Parc Taulí
Manel Esteller: Institut d’Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L’Hospitalet de Llobregat
David Monk: Institut d’Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L’Hospitalet de Llobregat

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: Abstract It has been postulated that imprinting aberrations are common in tumors. To understand the role of imprinting in cancer, we have characterized copy-number and methylation in over 280 cancer cell lines and confirm our observations in primary tumors. Imprinted differentially methylated regions (DMRs) regulate parent-of-origin monoallelic expression of neighboring transcripts in cis. Unlike single-copy CpG islands that may be prone to hypermethylation, imprinted DMRs can either loose or gain methylation during tumorigenesis. Here, we show that methylation profiles at imprinted DMRs often not represent genuine epigenetic changes but simply the accumulation of underlying copy-number aberrations (CNAs), which is independent of the genome methylation state inferred from cancer susceptible loci. Our results reveal that CNAs also influence allelic expression as loci with copy-number neutral loss-of-heterozygosity or amplifications may be expressed from the appropriate parental chromosomes, which is indicative of maintained imprinting, although not observed as a single expression foci by RNA FISH.

Date: 2017
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DOI: 10.1038/s41467-017-00639-9

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