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Frequent methylation of HOXA9 gene in tumor tissues and plasma samples from human hepatocellular carcinomas

  • Chih-Chi Kuo , Ching-Yu Lin , Yu-Lueng Shih , Chung-Bao Hsieh , Pei-Yu Lin , Shuh-Bing Guan , Ming-Song Hsieh , Hung-Cheng Lai , Chien-Jen Chen and Ya-Wen Lin EMAIL logo
Published/Copyright: March 21, 2003
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Clinical Chemistry and Laboratory Medicine (CCLM)
From the journal Clinical Chemistry and Laboratory Medicine (CCLM) Volume 52 Issue 8

Abstract

Background: Aberrant DNA methylation is associated with the development of hepatocellular carcinoma (HCC), suggesting that gene methylation could be a potential biomarker for detection of HCC. The aim of this study is to identify potential biomarkers in HCC.

Methods: We used the Infinium methylation array and a DNA-pooling strategy to analyze the genome-wide methylation profile in HCC. Quantitative methylation-specific PCR (Q-MSP) was used to validate homeobox A9 (HOXA9) methylation in 29 normal controls, 100 HCC samples and adjacent non-tumor tissues and in 74 plasma samples, including 40 patients with HCC.

Results: Ten genes (HOXA9, NEUROG1, TNFRSF10C, IRAK3, GFPT2, ZNF177, DPYSL4, ELOVL4, FSD1, and CACNA1G) showed differences in methylation between controls and HCCs. Of these, HOXA9 was significantly hypermethylated in HCCs (76.7%; 23/30) compared with controls (3.4%; 1/29). In addition, combination analysis of two- and three-gene sets for HCC detection showed greater sensitivity (90%–96.7%) and comparable specificity (93.1%–96.6%) to each individual gene (33.3%–76.7% and 55.2%–100.0%). HOXA9 methylation was further validated by Q-MSP in two independent set of clinical samples including 100 HCC and paired non-tumor tissues. Further, HOXA9 methylation could be detected in plasma from HCC patients (n=40) but not in normal plasma (n=34) (p<0.0005). Combined testing (either parameter positive) for α-fetoprotein (AFP, a plasma protein biomarker) and HOXA9 methylation showed greater sensitivity (94.6%) for detection of HCC than AFP alone (75.7%).

Conclusions: These data suggest that methylation of HOXA9 could be a helpful biomarker to assist in HCC detection.

Keywords: DNA methylation; HCC biomarker; HOXA9; methylation array
Corresponding author: Ya-Wen Lin, PhD, Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No. 161, Section 6, Min-Chuan East Road, Taipei, 114, Taiwan, Fax: +886-2-87917654, E-mail: ;

Acknowledgments

We would like to thank TLCN for providing tissue samples and related clinical data (all are anonymous) for our research work. This network currently includes five major medical centers (National Taiwan University Hospital, Chang-Gung Memorial Hospital-Linko, Veteran General Hospital-Taichung, Chang-Gung Memorial Hospital-Kaohsiung, and Veteran General Hospital -Kaohsiung). TLCN is supported by grants from National Science Council since 2005 till now (NSC 100-2325-B-182-006) and National Health Research Institutes, Taiwan. The authors are grateful to Mr. Chia-Hsin Lin, Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan, ROC, for the assistance on Q-MSP and Dr. Yu-Ching Chou, School of Public Health, National Defense Medical Center, Taipei, Taiwan, ROC, for the assistance on statistical analysis. This work was supported in part by the following grants: NSC 100-2622-B-038-003-CC2 and NSC 99-3112-B-016-003 from the National Science Council, Taiwan, Republic of China, and the Liver Disease Prevention and Treatment Research Foundation, Taiwan, Republic of China.

Conflict of interest statement

Authors’ conflict of interest disclosure: The authors stated that there are no conflicts of interest regarding the publication of this article. Research funding played no role in thestudy design; in the collection, analysis, and interpretationof data; in the writing of the report; or in the decision tosubmit the report for publication.

Research funding: None declared.

Employment or leadership: None declared.

Honorarium: None declared.

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Received: 2013-9-18
Accepted: 2014-2-11
Published Online: 2003-3-21
Published in Print: 2014-8-1

©2014 by Walter de Gruyter Berlin/Boston

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  2. Editorial
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  20. Reference Values
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  22. Cancer Diagnostics
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  24. Importance of promoter methylation of GATA4 and TP53 genes in endometrioid carcinoma of endometrium
  25. Frequent methylation of HOXA9 gene in tumor tissues and plasma samples from human hepatocellular carcinomas
  26. Letters to the Editor
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  28. A questionnaire study among nurses: awareness of blood and urine sample collection procedures
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  30. Laboratory automation: how will you select the boarding assays?
  31. Improvement and evaluation of a 1,2-dioleoylglycerol method for measuring pancreatic lipase catalytic activity in serum
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https://doi.org/10.1515/cclm-2013-0780
Keywords for this article
DNA methylation; HCC biomarker; HOXA9; methylation array

Articles in the same Issue

  1. Frontmatter
  2. Editorial
  3. Colorectal cancer and screening programs: not only analytical issues
  4. Reviews
  5. Laboratory diagnostics of inherited platelet disorders
  6. Reticulated platelets: analytical aspects and clinical utility
  7. Genetics and Molecular Diagnostics
  8. Advanced tools for BRCA1/2 mutational screening: comparison between two methods for large genomic rearrangements (LGRs) detection
  9. General Clinical Chemistry and Laboratory Medicine
  10. Establishing, harmonizing and analyzing critical values in a large academic health center
  11. Standardization of DiaSorin and Roche automated third generation PTH assays with an International Standard: impact on clinical populations
  12. First fully automated immunoassay for anti-Müllerian hormone
  13. A multicenter evaluation of dysthyroxinemia in a defined patient cohort
  14. New biomarkers in diagnosis of early onset preeclampsia and imminent delivery prognosis
  15. Soluble Fms-like tyrosine kinase-1 to placental growth factor ratio in mid-pregnancy as a predictor of preterm preeclampsia in asymptomatic pregnant women
  16. Development of a new immunoassay for the detection of ethyl glucuronide (EtG) in meconium: validation with authentic specimens analyzed using LC-MS/MS. Preliminary results
  17. Optimizing centrifugation of coagulation samples in laboratory automation
  18. Evaluation of the automated coagulation analyzer CS-5100 and its utility in high throughput laboratories
  19. A new sampling device for faecal immunochemical testing: haemoglobin stability is still an open issue
  20. Reference Values
  21. Faecal haemoglobin concentrations vary with sex and age, but data are not transferable across geography for colorectal cancer screening
  22. Cancer Diagnostics
  23. Enhanced miR-182 transcription is a predictor of poor overall survival in colorectal adenocarcinoma patients
  24. Importance of promoter methylation of GATA4 and TP53 genes in endometrioid carcinoma of endometrium
  25. Frequent methylation of HOXA9 gene in tumor tissues and plasma samples from human hepatocellular carcinomas
  26. Letters to the Editor
  27. Further comments on “Critical review of laboratory investigations in clinical practice guidelines: proposals for the description of investigation”
  28. A questionnaire study among nurses: awareness of blood and urine sample collection procedures
  29. Measurement uncertainty and clinical interpretation of measurement results
  30. Laboratory automation: how will you select the boarding assays?
  31. Improvement and evaluation of a 1,2-dioleoylglycerol method for measuring pancreatic lipase catalytic activity in serum
  32. The novel variant p.Ser465Leu in the PCSK9 gene does not account for the decreased LDLR activity in members of a FH family
  33. 1,5 Anhydroglucitol serum concentration as a biomarker for screening gestational diabetes in early pregnancy
  34. A rare condition: IgE type monoclonal gammopathy of undetermined significance
  35. Laboratory analysis of intraosseous blood: bad to the bone?
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