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Identification of genes and pathways, including the CXCL2 axis, altered by DNA methylation in hepatocellular carcinoma

  • Sophia Subat
  • Kaoru Mogushi
  • Mahmut Yasen
  • Takashi Kohda
  • Yuichi IshikawaEmail author
  • Hiroshi Tanaka
Original Article – Cancer Research
  • 79 Downloads

Abstract

Purpose

Recent genetic studies have suggested that tumor suppressor genes are often silenced during carcinogenesis via epigenetic modification caused by methylation of promoter CpG islands. Here, we characterized genes inactivated by DNA methylation in human hepatocellular carcinoma (HCC) to identify the genes and pathways involved in DNA methylation in hepatocellular carcinoma.

Methods

Eight HCC-derived cell lines were treated with a DNA demethylating agent, 5-aza-2′-deoxycytidine. Additionally, 100 pairs of primary HCC and adjacent non-cancerous tissues as well as 15 normal liver tissues were analyzed by comprehensive gene expression analysis using microarrays. Moreover, gene set enrichment analysis identified the major molecular pathways associated with DNA methylation. Validation of gene expression and DNA methylation status was performed by real-time PCR after bisulfite modification.

Results

We showed that CXCL2, an immune-related chemokine, expression was significantly downregulated in tumor tissues and also significantly upregulated by DAC treatment in cell lines. Furthermore, we observed a statistically significant difference in methylation status between normal liver tissues and tumor tissues (P < 0.05). In addition, tumors with higher CXCL2 expression included significantly more numbers of multiple tumors than the lower expression group.

Conclusions

We identified CXCL2, an immune-related chemokine, decreased in hepatocellular carcinoma and the regulation mechanism may be controlled by methylation. Further studies should be warranted to examine if and to what extent the gene is actually suppressed by methylation and if there is a possibility that the CXCL2 axis plays a role for diagnosis and treatment of hepatocellular carcinoma.

Keywords

Hepatocellular carcinoma DNA methylation Tumor suppressor genes CXCL2 Inflammation 

Abbreviations

ATF3

Activating transcription factor 3

CGIs

CpG islands

CXCL2

Chemokine (C-X-C motif) ligand 2

DAC

5-aza-2′-deoxycytidine

EMT

Epithelial–mesenchymal transition

FC

Fold change

FDR

False discovery rate

GRO

Growth-related oncogene

GSEA

Gene set enrichment analysis

HCC

Hepatocellular carcinoma

JUNB

Jun B proto-oncogene

KEGG

Kyoto Encyclopedia of Genes and Genomes

MSP

Methylation specific PCR

OS

Overall survival

PCR

Polymerase chain reaction

PTGS2

Prostaglandin-endoperoxide synthase 2

RFS

Recurrence-free survival

RMA

Robust multiarray average

SD

Standard deviation

TFBS

Transcription factor binding site

TGF-β

Transforming growth factor-β

THBS1

Thrombospondin 1

TSGs

Tumor suppressor genes

Notes

Authors’ contributions

All authors had full access to the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis. Conceptualization: SS, MY and HT Methodology, KM, MY and TK Investigation, SS, KM and MY Formal Analysis, SS and KM Resources, KM, TK and HT Writing—Original Draft, SS Writing-Review & Editing, KM and YI Visualization, SS Supervision, KM and YI Funding Acquisition KM and YI.

Funding

This work was supported partly by JSPS KAKENHI Grant Number: JP26870175 (KM), JSPS KAKENHI Grant Number: 15H04714 (YI).

Compliance with ethical standards

Conflict of interest

Yuichi Ishikawa received research grants from Daiichi Sankyo Co., Ltd. and Ono Pharmaceutical Co., Ltd., as well as he is a consultant of Fujirebio Inc. All other authors declare no conflicts of interest.

Ethical approval

This article does not contain any studies with animals performed by any of the authors.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

432_2018_2824_MOESM1_ESM.docx (617 kb)
Supplementary material 1 (DOCX 617 KB)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Systems Biology, Graduate School of Biomedical ScienceTokyo Medical and Dental UniversityTokyoJapan
  2. 2.Department of Epigenetics, Graduate School of Biomedical ScienceTokyo Medical and Dental UniversityTokyoJapan
  3. 3.Division of PathologyThe Cancer Institute, Japanese Foundation for Cancer ResearchTokyoJapan
  4. 4.Intractable Disease Research Center, Graduate School of MedicineJuntendo UniversityTokyoJapan
  5. 5.Department of SurgeryXinjiang Medical University Affiliated Tumor HospitalUrumqiChina

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