Loci-specific differences in blood DNA methylation in HBV-negative populations at risk for hepatocellular carcinoma development

Katarzyna Lubecka, Kirsty Flower, Megan Beetch, Jay Qiu, Lucinda Kurzava, Hannah Buvala, Adam Ruhayel, Samer Gawrieh, Suthat Liangpunsakul, Tracy Gonzalez, George McCabe, Naga Chalasani, James M. Flanagan, Barbara Stefanska

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Late onset of clinical symptoms in hepatocellular carcinoma (HCC) results in late diagnosis and poor disease outcome. Approximately 85% of individuals with HCC have underlying liver cirrhosis. However, not all cirrhotic patients develop cancer. Reliable tools that would distinguish cirrhotic patients who will develop cancer from those who will not are urgently needed. We used the Illumina HumanMethylation450 BeadChip microarray to test whether white blood cell DNA, an easily accessible source of DNA, exhibits site-specific changes in DNA methylation in blood of diagnosed HCC patients (post-diagnostic, 24 cases, 24 controls) and in prospectively collected blood specimens of HCC patients who were cancer-free at blood collection (pre-diagnostic, 21 cases, 21 controls). Out of 22 differentially methylated loci selected for validation by pyrosequencing, 19 loci with neighbouring CpG sites (probes) were confirmed in the pre-diagnostic study group and subjected to verification in a prospective cirrhotic cohort (13 cases, 23 controls). We established for the first time 9 probes that could distinguish HBV-negative cirrhotic patients who subsequently developed HCC from those who stayed cancer-free. These probes were identified within regulatory regions of BARD1, MAGEB3, BRUNOL5, FXYD6, TET1, TSPAN5, DPPA5, KIAA1210, and LSP1. Methylation levels within DPPA5, KIAA1210, and LSP1 were higher in prospective samples from HCC cases vs. cirrhotic controls. The remaining probes were hypomethylated in cases compared with controls. Using blood as a minimally invasive material and pyrosequencing as a straightforward quantitative method, the established probes have potential to be developed into a routine clinical test after validation in larger cohorts.

Original languageEnglish (US)
JournalEpigenetics
DOIs
StateAccepted/In press - Jan 1 2018

Fingerprint

DNA Methylation
Hepatocellular Carcinoma
Neoplasms
Nucleic Acid Regulatory Sequences
Delayed Diagnosis
DNA
Liver Cirrhosis
Methylation
Leukocytes

Keywords

  • cirrhotic populations
  • DNA methylation
  • early detection
  • HCC

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research

Cite this

Loci-specific differences in blood DNA methylation in HBV-negative populations at risk for hepatocellular carcinoma development. / Lubecka, Katarzyna; Flower, Kirsty; Beetch, Megan; Qiu, Jay; Kurzava, Lucinda; Buvala, Hannah; Ruhayel, Adam; Gawrieh, Samer; Liangpunsakul, Suthat; Gonzalez, Tracy; McCabe, George; Chalasani, Naga; Flanagan, James M.; Stefanska, Barbara.

In: Epigenetics, 01.01.2018.

Research output: Contribution to journalArticle

Lubecka, Katarzyna ; Flower, Kirsty ; Beetch, Megan ; Qiu, Jay ; Kurzava, Lucinda ; Buvala, Hannah ; Ruhayel, Adam ; Gawrieh, Samer ; Liangpunsakul, Suthat ; Gonzalez, Tracy ; McCabe, George ; Chalasani, Naga ; Flanagan, James M. ; Stefanska, Barbara. / Loci-specific differences in blood DNA methylation in HBV-negative populations at risk for hepatocellular carcinoma development. In: Epigenetics. 2018.
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AU - Buvala, Hannah

AU - Ruhayel, Adam

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AU - Gonzalez, Tracy

AU - McCabe, George

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AU - Stefanska, Barbara

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AB - Late onset of clinical symptoms in hepatocellular carcinoma (HCC) results in late diagnosis and poor disease outcome. Approximately 85% of individuals with HCC have underlying liver cirrhosis. However, not all cirrhotic patients develop cancer. Reliable tools that would distinguish cirrhotic patients who will develop cancer from those who will not are urgently needed. We used the Illumina HumanMethylation450 BeadChip microarray to test whether white blood cell DNA, an easily accessible source of DNA, exhibits site-specific changes in DNA methylation in blood of diagnosed HCC patients (post-diagnostic, 24 cases, 24 controls) and in prospectively collected blood specimens of HCC patients who were cancer-free at blood collection (pre-diagnostic, 21 cases, 21 controls). Out of 22 differentially methylated loci selected for validation by pyrosequencing, 19 loci with neighbouring CpG sites (probes) were confirmed in the pre-diagnostic study group and subjected to verification in a prospective cirrhotic cohort (13 cases, 23 controls). We established for the first time 9 probes that could distinguish HBV-negative cirrhotic patients who subsequently developed HCC from those who stayed cancer-free. These probes were identified within regulatory regions of BARD1, MAGEB3, BRUNOL5, FXYD6, TET1, TSPAN5, DPPA5, KIAA1210, and LSP1. Methylation levels within DPPA5, KIAA1210, and LSP1 were higher in prospective samples from HCC cases vs. cirrhotic controls. The remaining probes were hypomethylated in cases compared with controls. Using blood as a minimally invasive material and pyrosequencing as a straightforward quantitative method, the established probes have potential to be developed into a routine clinical test after validation in larger cohorts.

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