DNA methylome analyses implicate fallopian tube epithelia as the origin for high-grade serous ovarian cancer

David L Klinkebiel, Wa Zhang, Stacey N. Akers, Kunle Odunsi, Adam R Karpf

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Abstract

High-grade serous ovarian cancer (HGSC) is the most common and lethal form of epithelial ovarian cancer (EOC). Two distinct tissues have been suggested as the tissue of origin: ovarian surface epithelia (OSE) and fallopian tube epithelia (FTE). We hypothesized that the DNA methylome of HGSC should more closely resemble the methylome of its tissue of origin. To this end, we profiled HGSC (n = 10), and patient-matched OSE and FTE (n = 5) primary fresh-frozen tissues, and analyzed the DNA methylome using Illumina 450K arrays (n = 20) and Agilent Sure Select methyl-seq (n = 7). Methylomes were compared using statistical analyses of differentially methylated CpG sites (DMC) and differentially methylated regions (DMR). In addition, methylation was evaluated within a variety of different genomic contexts, including CpG island shores and Homeobox (HOX) genes, due to their roles in tissue specification. Publicly available HGSC methylome data (n = 628) were interrogated to provide additional comparisons with FTE and OSE for validation. These analyses revealed that HGSC and FTE methylomes are significantlyand consistently more highly conserved than are HGSC and OSE. Pearson correlations and hierarchal clustering of genes, promoters, CpG islands, CpG island shores, and HOX genes all revealed increased relatedness of HGSC and FTE methylomes. Thus, these findings reveal that the landscape of FTE more closely resembles HGSC, the most common and deadly EOC subtype. Implications: DNA methylome analyses support the hypothesis that HGSC arise from the fallopian tube and that due to its tissuespecificity and biochemical stability, interrogation of the methylome may be a valuable approach to examine cell/tissue lineage in cancer.

Original languageEnglish (US)
Pages (from-to)787-794
Number of pages8
JournalMolecular Cancer Research
Volume14
Issue number9
DOIs
StatePublished - Sep 1 2016

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Fallopian Tubes
Ovarian Neoplasms
Epithelium
DNA
Fallopian Tube Neoplasms
CpG Islands
Homeobox Genes
Cell Lineage
Methylation
Cluster Analysis

ASJC Scopus subject areas

  • Molecular Biology
  • Oncology
  • Cancer Research

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DNA methylome analyses implicate fallopian tube epithelia as the origin for high-grade serous ovarian cancer. / Klinkebiel, David L; Zhang, Wa; Akers, Stacey N.; Odunsi, Kunle; Karpf, Adam R.

In: Molecular Cancer Research, Vol. 14, No. 9, 01.09.2016, p. 787-794.

Research output: Contribution to journalArticle

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abstract = "High-grade serous ovarian cancer (HGSC) is the most common and lethal form of epithelial ovarian cancer (EOC). Two distinct tissues have been suggested as the tissue of origin: ovarian surface epithelia (OSE) and fallopian tube epithelia (FTE). We hypothesized that the DNA methylome of HGSC should more closely resemble the methylome of its tissue of origin. To this end, we profiled HGSC (n = 10), and patient-matched OSE and FTE (n = 5) primary fresh-frozen tissues, and analyzed the DNA methylome using Illumina 450K arrays (n = 20) and Agilent Sure Select methyl-seq (n = 7). Methylomes were compared using statistical analyses of differentially methylated CpG sites (DMC) and differentially methylated regions (DMR). In addition, methylation was evaluated within a variety of different genomic contexts, including CpG island shores and Homeobox (HOX) genes, due to their roles in tissue specification. Publicly available HGSC methylome data (n = 628) were interrogated to provide additional comparisons with FTE and OSE for validation. These analyses revealed that HGSC and FTE methylomes are significantlyand consistently more highly conserved than are HGSC and OSE. Pearson correlations and hierarchal clustering of genes, promoters, CpG islands, CpG island shores, and HOX genes all revealed increased relatedness of HGSC and FTE methylomes. Thus, these findings reveal that the landscape of FTE more closely resembles HGSC, the most common and deadly EOC subtype. Implications: DNA methylome analyses support the hypothesis that HGSC arise from the fallopian tube and that due to its tissuespecificity and biochemical stability, interrogation of the methylome may be a valuable approach to examine cell/tissue lineage in cancer.",
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