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Aberrant methylation of tumour suppressor genes WT1, GATA5 and PAX5 in hepatocellular carcinoma

  • Martin Mžik , Marcela Chmelařová , Stanislav John , Jan Laco , Ondřej Slabý , Igor Kiss , Lucia Bohovicová , Vladimír Palička and Jana Nekvindová ORCID logo EMAIL logo
Published/Copyright: May 12, 2016
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Clinical Chemistry and Laboratory Medicine (CCLM)
From the journal Clinical Chemistry and Laboratory Medicine (CCLM) Volume 54 Issue 12

Abstract

Background:

Aberrant hypermethylation of tumour suppressor genes (TSGs) occurring in hepatocellular carcinoma (HCC) could provide a mean of molecular characterisation of this cancer. The aim of this study was to investigate promoter methylation and gene expression of selected TSGs in HCC to identify candidate genes for further validation as potential biomarkers.

Methods:

Methylation-specific multiplex ligation-dependent probe amplification method was used to measure the methylation status of 25 TSGs in 49 HCC samples and 36 corresponding non-cancerous liver tissue samples. Relative expression of the differentially methylated genes was assessed at the mRNA level using quantitative PCR.

Results:

We observed a significantly higher methylation in genes WT1, PAX5, PAX6, PYCARD and GATA5 in HCC compared with control samples. The expression of PAX5 was significantly decreased by methylation; conversely methylation of WT1 was associated with higher mRNA levels. Methylation of GATA5 was significantly associated with overall survival and methylation of WT1 and PAX5 significantly varied between patients with ALBI score 1 vs. 2+3. Moreover, PAX5 was significantly more methylated in patients with tumour grade 2+3 vs. grade 1, and methylation of the PAX5 correlated with the patient’s age at the time of diagnosis.

Conclusions:

HCC evince aberrant promoter methylation of WT1, PAX5, PAX6, PYCARD and GATA5 genes. Correlation between GATA5, WT1 and PAX5 methylation and clinical/histological parameters is suggestive of applicability of these markers in non-invasive (epi)genetic testing in HCC.

Keywords: DNA methylation; hepatocellular carcinoma (HCC); methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA); promoter; tumour suppressor gene
Corresponding author: Jana Nekvindová, PhD, Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic, Phone: (+420) 495 832 767

Acknowledgments:

The authors are grateful to Ian McColl MD, PhD for language correction of the manuscript and to Ivana Bubancova, MSc. for help with qPCR.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work has been supported by MH CZ – DRO (UHHK, 00179906), by the program PRVOUK P37/11 and by program SVV 260181.

  3. Employment or leadership: None declared.

  4. Honorarium: None declared.

  5. Competing interest: The funding organisation(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.

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Received: 2015-12-3
Accepted: 2016-4-11
Published Online: 2016-5-12
Published in Print: 2016-12-1

©2016 Walter de Gruyter GmbH, Berlin/Boston

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https://doi.org/10.1515/cclm-2015-1198
Keywords for this article
DNA methylation; hepatocellular carcinoma (HCC); methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA); promoter; tumour suppressor gene

Articles in the same Issue

  1. Frontmatter
  2. Editorial
  3. Biomarkers, inflammation and cancer: where to go?
  4. Review
  5. Analysis, detection and quantitation of mixed cryoglobulins in HCV infection: brief review and case examples
  6. Mini Reviews
  7. Calcitonin measurement and immunoassay interference: a case report and literature review
  8. Exosomal non-coding RNAs: a promising cancer biomarker
  9. Opinion Paper
  10. Towards a new paradigm in laboratory medicine: the five rights
  11. EFLM Recommendation
  12. Recommendation for the review of biological reference intervals in medical laboratories
  13. IFCC Position Paper
  14. Assuring the quality of interpretative comments in clinical chemistry
  15. General Clinical Chemistry and Laboratory Medicine
  16. The effect of centrifugation speed and time on pre-analytical platelet activation
  17. An assessment of clinical laboratory performance for the determination of manganese in blood and urine
  18. Evaluation of antiphospholipid antibody assays using latent class analysis to address the lack of a reference standard
  19. Evaluation of the hypochromic erythrocyte and reticulocyte hemoglobin content provided by the Sysmex XE-5000 analyzer in diagnosis of iron deficiency erythropoiesis
  20. Cancer Diagnosis
  21. Identifying risk in the use of tumor markers to improve patient safety
  22. Association between Echinococcus granulosus infection and cancer risk – a pilot study in Cyprus
  23. Dynamic change of the systemic immune inflammation index predicts the prognosis of patients with hepatocellular carcinoma after curative resection
  24. Aberrant methylation of tumour suppressor genes WT1, GATA5 and PAX5 in hepatocellular carcinoma
  25. Cardiovascular Diseases
  26. High homocysteine and low folate plasma concentrations are associated with cardiovascular events but not bleeding during warfarin treatment
  27. Hemolysis and Coagulation
  28. Hemolysis rates in blood samples: differences between blood collected by clinicians and nurses and the effect of phlebotomy training
  29. Letters to the Editor
  30. Harmonisation of the laboratory testing process: need for a coordinated approach
  31. Pseudohyperkalemia due to severe leukocytosis: case presentation
  32. When obtaining a blood sample from the right arm was not the right thing to do: a case of elevated parathyroid hormone levels 27 years after thyroidectomy
  33. Raising awareness of assay compatibility with heparinized plasma
  34. Improved protocol for extraction of genomic DNA from formalin-fixed paraffin-embedded tissue samples without the use of xylene
  35. Effect of refrigeration, centrifugation, acidification, heat treatment and storage on urine calcium, magnesium and phosphate
  36. Letter in response to: Identifying risk in the use of tumor markers to improve patient safety
  37. Letter to the Editor in reply to Dayyani and Morgenstern’s comment on the article “Identifying risk in the use of tumor markers to improve patient safety”
  38. Level of red cell distribution width is affected by various factors
  39. Red blood cell distribution: an index without additional cost in estimating the prognosis of acute pancreatitis
  40. Testing of total 25(OH)vitamin D: agreement and discrepant cases between Cobas® 8000 and Liaison® XL methods
  41. Expression profiling and ontology analysis of circulating long non-coding RNAs in septic acute kidney injury patients
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