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Prognostic value of Iroquois homeobox 1 methylation in non-small cell lung cancers

Genes & Genomics volume 42, pages 571–579 (2020)Cite this article

Abstract

Background

Non-small cell lung cancer (NSCLC) poses a great threat to human health. DNA methylation abnormalities play a central role in the development and outcome of most human malignancies, providing potential biomarkers for diagnosis and prognosis. Iroquois homeobox 1 (IRX1) can act as a tumor suppressor or promoter depending on the tumor microenvironment, and its role in lung cancer is still controversial.

Objective

The purpose of this study was to investigate the biological role and prognostic value of IRX1 in NSCLC.

Methods

We examined the methylation status of IRX1 promoter in 146 tumors from patients with NSCLC using pyrosequencing and analyzed the association between methylation status and overall patient survival.

Results

A total of 37 cases (25.3%) showed IRX1 methylation-positive tumors when compared with matched normal tissues. No association between IRX1 expression level and methylation status was found in lung cancer cell lines. IRX1 methylation significantly correlated with smoking status and TP53 mutation. Patients with IRX1 methylation showed significantly longer survival than patients without methylation (log-rank P = 0.011). In a multivariate analysis of prognostic factors, IRX1 methylation in tumor samples was an independent prognostic factor (adjusted hazard ratio = 0.35, 95% confidence interval 0.17–0.73, P = 0.005).

Conclusion

These results suggest that IRX1 promoter methylation may be a tumor-associated event and an independent predictor of survival advantage in patients with NSCLC. Further large-scale studies are needed to confirm these findings.

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References

  • Bennett KL, Karpenko M, Lin MT, Claus R, Arab K, Dyckhoff G, Plinkert P, Herpel E, Smiraglia D, Plass C (2008) Frequently methylated tumor suppressor genes in head and neck squamous cell carcinoma. Cancer Res 68:4494–4499

    CAS  Article  Google Scholar 

  • Bennett KL, Romigh T, Eng C (2009) Disruption of Transforming growth factor-β signaling by five frequently methylated genes leads head and neck squamous cell carcinoma. Cancer Res 69:9301–9305

    CAS  Article  Google Scholar 

  • Bennett KL, Lee W, Lamarre E, Zhang X, Seth R, Scharpf J, Hunt J, Eng C (2010) HPV status-independent association of alcohol and tobacco exposure or prior radiation therapy with promoter methylation of FUSSEL18, EBF3, IRX1, and SEPT9, but not SLC5A8, in head and neck squamous cell carcinomas. Genes Chromosomes Cancer 49:319–326

    CAS  PubMed  Google Scholar 

  • Bert SA, Robinson MD, Strbenac D, Statham AL, Song JZ, Hulf T, Sutherland RL, Coolen MW, Stirzaker C, Clark SJ (2013) Regional activation of the cancer genome by long-range epigenetic remodeling. Cancer Cell 23:9–22

    CAS  Article  Google Scholar 

  • Braga LC, Silva LM, Ramos AP, Piedade JB, Vidigal PV, Traiman P, da Silva Filho AL (2014) Single CpG island methylation is not sufficient to maintain the silenced expression of CASPASE-8 apoptosis-related gene among women with epithelial ovarian cancer. Biomed Pharmacother 68:87–91

    CAS  Article  Google Scholar 

  • Cavodeassi F, Modolell J, Gomez-Skarmeta JL (2001) The Iroquois family of genes: from body building to neural pattering. Development 128:2847–2855

    CAS  PubMed  Google Scholar 

  • Chen C, Yin N, Yin B, Lu Q (2011) DNA methylation in thoracic neoplasms. Cancer Lett 301:7–16

    CAS  Article  Google Scholar 

  • Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25:1010–1022

    CAS  Article  Google Scholar 

  • Doi T, Lukosiute A, Ruttenstock E, Dingemann J, Puri P (2011) Expression of Iroquois genes is upregulated during early lung development in the nitrofen-induced pulmonary hypoplasia. J Pediatr Surg 46:62–66

    Article  Google Scholar 

  • Dor Y, Cedar H (2018) Principles of DNA methylation and their implications for biology and medicine. Lancet 392:777–786

    CAS  Article  Google Scholar 

  • Gao C, Zhung J, Zhou C, Ma K, Zhao M, Liu C, Liu L, Li H, Feng F, Sun C (2019) Prognostic value of aberrantly expressed methylation gene profiles in lung squamous cell carcinoma: a study based The Cancer Genome Atlas. J Cell Physiol 234:6519–6528

    CAS  Article  Google Scholar 

  • Gokul G, Khosla S (2013) DNA methylation and cancer. Subcell Biochem 61:597–625

    CAS  Article  Google Scholar 

  • Guo X, Liu W, Pan Y, Ni P, Ji J, Guo L, Zhang J, Wu J, Jiang J, Chen X et al (2010) Homeobox gene IRX1 is a tumor suppressor gene in gastric carcinoma. Oncogene 29:3908–3920

    CAS  Article  Google Scholar 

  • He Y, Huang Y, Li N, Yan H, Yang RF, Jiang L, Jiang XH, Cao B (2018) Expression of IRX1 in cervical cancer and its correlation with clinical stage of cervical cancer. Zhonghua Yi Xue Za Zhi 98:222–226

    CAS  PubMed  Google Scholar 

  • Illingworth RS, Bird AP (2009) CpG islands—‘a rough guide’. FEBS Lett 583:1713–1720

    CAS  Article  Google Scholar 

  • Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M et al (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41:178–186

    CAS  Article  Google Scholar 

  • Jankowska AM, Millward CL, Caldwell CW (2015) The potential of DNA modifications as biomarkers and therapeutic targets in oncology. Expert Rev Mol Diagn 15:1325–1337

    CAS  Article  Google Scholar 

  • Kim DS, Lee SM, Yoon GS, Choi JE, Park JY (2010) Infrequent hypermethylation of the PTEN gene in Korean non-small cell lung cancers. Cancer Sci 101:568–572

    CAS  Article  Google Scholar 

  • Kim DS, Lee WK, Park JY (2018) Hypermethylation of normal mucosa of esophagus-specific 1 is associated with an unfavorable prognosis in patients with non-small cell lung cancer. Oncol Lett 16:2409–2415

    PubMed  PubMed Central  Google Scholar 

  • Kim YH, Lee WK, Park JY, Kim DS (2015) Prognostic value of hepatoma-derived growth factor-related protein 3 (HRP-3) methylation in non-small cell lung cancer. Genes Genom 37:479–486

    CAS  Article  Google Scholar 

  • Kitchen MO, Bryan RT, Emes RD, Glossop JR, Luscombe C, Cheng KK, Zeegers MP, James ND, Devall AJ, Mein CA et al (2016) Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer. Epigenetics 11:237–246

    Article  Google Scholar 

  • Kuhn A, Loscher D, Marschalek R (2016) The IRX1/HOXA connection: insights into a novel t (4;11)-specific cancer mechanism. Oncotarget 7:35341–35352

    Article  Google Scholar 

  • Lee MK, Jeong EM, Kim JH, Rho SB, Lee EJ (2014) Aberrant methylation of the VIM promoter in uterine cervical squamous cell carcinoma. Oncology 86:359–368

    CAS  Article  Google Scholar 

  • Lessi F, Beggs A, de Palo M, Anti M, Macarone Palmieri R, Francesconi S, Gomes V, Bevilacqua G, Tomlinson I, Segditsas S (2010) Down-regulation of serum/glucocorticoid regulated kinase 1 in colorectal tumours is largely independent of promoter hypermethylation. PLoS One 5:e13840

    Article  Google Scholar 

  • Liu X, Zhang J, Liu L, Jiang Y, Ji J, Yan R, Zhu Z, Yu Y (2018) Protein arginine methyltransferase 5-mediated epigenetic silencing of IRX1 contributes to tumorigenicity and metastasis of gastric cancer. Biochim Biophys Acta Mol Basis Dis 1864:2835–2844

    CAS  Article  Google Scholar 

  • Lu F, Zhang HT (2011) DNA methylation and nonsmall cell lung cancer. Anat Rec 294:1787–1795

    CAS  Article  Google Scholar 

  • Lu J, Song G, Tang Q, Zou C, Han F, Zhao Z, Yong B, Yin J, Xu H, Xie X et al (2015) IRX1 hypomethylation promotes osteosarcoma metastasis via induction of CXCL14/NF-κB signaling. J Clin Investig 125:1839–1856

    Article  Google Scholar 

  • Ma X, Shang F, Zhu W, Lin Q (2017) CXCR4 expression varies significantly among different subtypes of glioblastoma multiforme (GBM) and its low expression or hypermethylation might predict favorable overall survival. Expert Rev Neurother 17:941–946

    CAS  Article  Google Scholar 

  • Mahoney SE, Yao Z, Keyes CC, Tapscott SJ, Diede SJ (2012) Genome-wide DNA methylation studies suggest distinct DNA methylation patterns in pediatric embryonal and alveolar rhabdomyosarcomas. Epigenetics 7:400–408

    CAS  Article  Google Scholar 

  • Marcinkiewicz KM, Gudas LJ (2014) Altered histone mark deposition and DNA methylation at homeobox genes in human oral squamous cell carcinoma. J Cell Physiol 229:1405–1416

    CAS  Article  Google Scholar 

  • Rodriguez-Seguel E, Alarcon P, Gomez-Skarmeta JL (2009) The Xenopus Irx genes are essential for neural patterning and define the border between prethalamus and thalamus through mutual antagonism with the anterior repressors Fezf and Arx. Dev Biol 329:258–268

    CAS  Article  Google Scholar 

  • Selamat SA, Chung BS, Girard L, Zhang W, Zhang Y, Campan M, Siegmund KD, Koss MN, Hagen JA, Lam WL et al (2012) Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res 22:1197–1211

    CAS  Article  Google Scholar 

  • Seok Y, Lee WK, Park JY, Kim DS (2019) TGFBI promoter methylation is associated with poor prognosis in lung adenocarcinoma patients. Mol Cells 42:161–165

    CAS  PubMed  PubMed Central  Google Scholar 

  • Siegel RL, Miller KD, Jemal A (2018) Cancer statistics 2018. CA Cancer J Clin 68:7–30

    Article  Google Scholar 

  • Spiro SG, Silvestri GA (2005) One hundred years of lung cancer. Am J Respir Crit Care Med 172:523–529

    Article  Google Scholar 

  • Tan Q, Wang G, Huang J, Ding Z, Luo Q, Mol T, Tao Q, Lu S (2013) Epigenomic analysis of lung adenocarcinoma reveals novel DNA methylation patterns associated with smoking. Onco Targets Ther 6:1471–1479

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yano T, Haro A, Shikada Y, Maruyama R, Maehara Y (2011) Non-small cell lung cancer in never smokers as a representative ‘non-smoking-associated lung cancer’: epidemiology and clinical features. Int J Clin Oncol 16:287–293

    CAS  Article  Google Scholar 

  • Yu W, Li X, Eliason S, Romero-Bustillos M, Ries RJ, Cao H, Amendt BA (2017) Irx1 regulates dental outer enamel epithelial and lung alveolar type II epithelial differentiation. Dev Biol 429:44–55

    CAS  Article  Google Scholar 

  • Zhang P, Liu N, Xu X, Wang Z, Cheng Y, Jin W, Wang X, Yang H, Liu H, Zhang Y et al (2018) Clinical significance of iroquois homeobox gene-IRX1 in human glioma. Mol Med Rep 17:4651–4656

    CAS  PubMed  Google Scholar 

  • Zhou C, Ye M, Ni S, Li Q, Ye D, Li J, Shen Z, Deng H (2018) DNA mehtylation biomarkers for head and neck squamous cell carcinoma. Epigenetics 13:398–409

    Article  Google Scholar 

Download references

Funding

This study was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) (No. NRF-2016R1D1A1B03931462).

Author information

Affiliations

  1. Department of Anatomy and BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, 2-101 Dongin-dong, Jung-gu, Daegu, 702-422, Republic of Korea

    Ji Yun Lee & Dong Sun Kim

  2. Department of Preventive Medicine, School of Medicine, Kyungpook National University, Daegu, 702-422, Republic of Korea

    Won Kee Lee

  3. Department of Internal Medicine, School of Medicine, Kyungpook National University, 2-101 Dongin-dong, Jung-gu, Daegu, 702-422, Republic of Korea

    Jae Yong Park

Authors
  1. Ji Yun Lee
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  2. Won Kee Lee
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  3. Jae Yong Park
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  4. Dong Sun Kim
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Contributions

JYL contributed to the experimental design and implementation, performed the experiments and data analysis, and drafted the manuscript. LWK performed statistical analyses. PJY and KDS contributed to experiment implementation, interpreted the patient data and modified the manuscript. All authors have read and approved the final manuscript.

Corresponding authors

Correspondence to Jae Yong Park or Dong Sun Kim.

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Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This study was approved by the Ethics Committee of KNUHl (No. 2014-04-210).

Informed consent

Written informed consent was obtained from all participants or their families prior to obtaining the samples.

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Lee, J.Y., Lee, W.K., Park, J.Y. et al. Prognostic value of Iroquois homeobox 1 methylation in non-small cell lung cancers. Genes Genom 42, 571–579 (2020). https://doi.org/10.1007/s13258-020-00925-9

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  • DOI: https://doi.org/10.1007/s13258-020-00925-9

Keywords

  • Non-small cell lung cancer
  • Hypermethylation
  • IRX1
  • Pyrosequencing
  • Prognosticator