Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors.

2.50
Hdl Handle:
http://hdl.handle.net/10033/267272
Title:
Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors.
Authors:
Neumann, Olaf; Kesselmeier, Miriam; Geffers, Robert; Pellegrino, Rossella; Radlwimmer, Bernhard; Hoffmann, Katrin; Ehemann, Volker; Schemmer, Peter; Schirmacher, Peter; Lorenzo Bermejo, Justo; Longerich, Thomas
Abstract:
To identify new tumor-suppressor gene candidates relevant for human hepatocarcinogenesis, we performed genome-wide methylation profiling and vertical integration with array-based comparative genomic hybridization (aCGH), as well as expression data from a cohort of well-characterized human hepatocellular carcinomas (HCCs). Bisulfite-converted DNAs from 63 HCCs and 10 healthy control livers were analyzed for the methylation status of more than 14,000 genes. After defining the differentially methylated genes in HCCs, we integrated their DNA copy-number alterations as determined by aCGH data and correlated them with gene expression to identify genes potentially silenced by promoter hypermethylation. Aberrant methylation of candidates was further confirmed by pyrosequencing, and methylation dependency of silencing was determined by 5-aza-2'-deoxycytidine (5-aza-dC) treatment. Methylation profiling revealed 2,226 CpG sites that showed methylation differences between healthy control livers and HCCs. Of these, 537 CpG sites were hypermethylated in the tumor DNA, whereas 1,689 sites showed promoter hypomethylation. The hypermethylated set was enriched for genes known to be inactivated by the polycomb repressive complex 2, whereas the group of hypomethylated genes was enriched for imprinted genes. We identified three genes matching all of our selection criteria for a tumor-suppressor gene (period homolog 3 [PER3], insulin-like growth-factor-binding protein, acid labile subunit [IGFALS], and protein Z). PER3 was down-regulated in human HCCs, compared to peritumorous and healthy liver tissues. 5-aza-dC treatment restored PER3 expression in HCC cell lines, indicating that promoter hypermethylation was indeed responsible for gene silencing. Additionally, functional analysis supported a tumor-suppressive function for PER3 and IGFALS in vitro. CONCLUSION: The present study illustrates that vertical integration of methylation data with high-resolution genomic and transcriptomic data facilitates the identification of new tumor-suppressor gene candidates in human HCC.
Affiliation:
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
Citation:
Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors. 2012, 56 (5):1817-27 Hepatology
Journal:
Hepatology (Baltimore, Md.)
Issue Date:
Nov-2012
URI:
http://hdl.handle.net/10033/267272
DOI:
10.1002/hep.25870
PubMed ID:
22689435
Type:
Article
Language:
en
ISSN:
1527-3350
Appears in Collections:
publications of the research group genomeanalytics (GMAK)

Full metadata record

DC FieldValue Language
dc.contributor.authorNeumann, Olafen_GB
dc.contributor.authorKesselmeier, Miriamen_GB
dc.contributor.authorGeffers, Roberten_GB
dc.contributor.authorPellegrino, Rossellaen_GB
dc.contributor.authorRadlwimmer, Bernharden_GB
dc.contributor.authorHoffmann, Katrinen_GB
dc.contributor.authorEhemann, Volkeren_GB
dc.contributor.authorSchemmer, Peteren_GB
dc.contributor.authorSchirmacher, Peteren_GB
dc.contributor.authorLorenzo Bermejo, Justoen_GB
dc.contributor.authorLongerich, Thomasen_GB
dc.date.accessioned2013-01-28T10:30:15Z-
dc.date.available2013-01-28T10:30:15Z-
dc.date.issued2012-11-
dc.identifier.citationMethylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors. 2012, 56 (5):1817-27 Hepatologyen_GB
dc.identifier.issn1527-3350-
dc.identifier.pmid22689435-
dc.identifier.doi10.1002/hep.25870-
dc.identifier.urihttp://hdl.handle.net/10033/267272-
dc.description.abstractTo identify new tumor-suppressor gene candidates relevant for human hepatocarcinogenesis, we performed genome-wide methylation profiling and vertical integration with array-based comparative genomic hybridization (aCGH), as well as expression data from a cohort of well-characterized human hepatocellular carcinomas (HCCs). Bisulfite-converted DNAs from 63 HCCs and 10 healthy control livers were analyzed for the methylation status of more than 14,000 genes. After defining the differentially methylated genes in HCCs, we integrated their DNA copy-number alterations as determined by aCGH data and correlated them with gene expression to identify genes potentially silenced by promoter hypermethylation. Aberrant methylation of candidates was further confirmed by pyrosequencing, and methylation dependency of silencing was determined by 5-aza-2'-deoxycytidine (5-aza-dC) treatment. Methylation profiling revealed 2,226 CpG sites that showed methylation differences between healthy control livers and HCCs. Of these, 537 CpG sites were hypermethylated in the tumor DNA, whereas 1,689 sites showed promoter hypomethylation. The hypermethylated set was enriched for genes known to be inactivated by the polycomb repressive complex 2, whereas the group of hypomethylated genes was enriched for imprinted genes. We identified three genes matching all of our selection criteria for a tumor-suppressor gene (period homolog 3 [PER3], insulin-like growth-factor-binding protein, acid labile subunit [IGFALS], and protein Z). PER3 was down-regulated in human HCCs, compared to peritumorous and healthy liver tissues. 5-aza-dC treatment restored PER3 expression in HCC cell lines, indicating that promoter hypermethylation was indeed responsible for gene silencing. Additionally, functional analysis supported a tumor-suppressive function for PER3 and IGFALS in vitro. CONCLUSION: The present study illustrates that vertical integration of methylation data with high-resolution genomic and transcriptomic data facilitates the identification of new tumor-suppressor gene candidates in human HCC.en_GB
dc.language.isoenen
dc.rightsArchived with thanks to Hepatology (Baltimore, Md.)en_GB
dc.subject.meshAdolescenten_GB
dc.subject.meshAdulten_GB
dc.subject.meshAgeden_GB
dc.subject.meshAntimetabolites, Antineoplasticen_GB
dc.subject.meshAzacitidineen_GB
dc.subject.meshBlood Proteinsen_GB
dc.subject.meshCarcinoma, Hepatocellularen_GB
dc.subject.meshCarrier Proteinsen_GB
dc.subject.meshCase-Control Studiesen_GB
dc.subject.meshCell Line, Tumoren_GB
dc.subject.meshComparative Genomic Hybridizationen_GB
dc.subject.meshCpG Islandsen_GB
dc.subject.meshDNA Methylationen_GB
dc.subject.meshDown-Regulationen_GB
dc.subject.meshFemaleen_GB
dc.subject.meshGene Expression Profilingen_GB
dc.subject.meshGene Silencingen_GB
dc.subject.meshGenes, Tumor Suppressoren_GB
dc.subject.meshGlycoproteinsen_GB
dc.subject.meshHumansen_GB
dc.subject.meshLiveren_GB
dc.subject.meshLiver Neoplasmsen_GB
dc.subject.meshMaleen_GB
dc.subject.meshMiddle Ageden_GB
dc.subject.meshPeriod Circadian Proteinsen_GB
dc.subject.meshPromoter Regions, Geneticen_GB
dc.subject.meshYoung Adulten_GB
dc.titleMethylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors.en
dc.typeArticleen
dc.contributor.departmentInstitute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.en_GB
dc.identifier.journalHepatology (Baltimore, Md.)en_GB

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