Determining the methylation status of the promoter regions of MARCH11, HOXA9, PTGDR, and UNCX genes in patients with non-small cell lung cancer

The aim of this study was to determine the methylation status of the promoter regions of MARCH11, HOXA9, PTGDR, and UNCX genes in the tumor and non-tumor lung tissue in patients with non-small cell lung cancer (NSCLC). A relative level of methylation of the promoter regions of MARCH11, HOXA9, PTGDR, and UNCX genes was determined by the quantitative methylation-specific PCR in 73 patients with NSCLC. The quantitative methylation-specific reaction was performed both for tumor tissue samples and non-tumor tissue samples of the same patient. For each of the samples, a reaction was set both by the investigated genes (MARCH11, UNCX, HOXA9, and PTGDR) and by the reference beta-actin gene (β-actin). Positive levels of methylation of the HOXA9 gene were established for 83.5 % patients; the MARCH11 gene – for 80.8 % patients; the PTGDR gene – for 68.4 % patients; the UNCX gene – for 84.9 % patients. In the study group of patients with NSCLC, significant differences were found in the relative levels of methylation of the promoter regions of MARCH11, HOXA9, PTGDR, and UNCX genes in the tumor and non-tumor lung tissue. The data suggest that hypermethylation of MARCH11, HOXA9, PTGDR, and UNCX genes may play a role in NSCLC tumor progression.

1. Zhang L., Lu Q., Chang C. Epigenetics in health and disease. Advances in Experimental Medicine and Biology, 2020, vol. 1253, pp. 3–55. https://doi.org/10.1007/978-981-15-3449-2_1

2. Jaffe A. E., Murakami P., Lee H., Leek J. T., Fallin M. D., Feinberg A. P., Irizarry R. A. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. International Journal of Epidemiology, 2012, vol. 41, no. 1, pp. 200–209. https://doi.org/10.1093/ije/dyr238

3. Diaz-Lagares A, Mendez-Gonzalez J., Hervas D., Saigi M., Pajares M. J., Garcia D., Crujerias A. B., Pio R., Montuenga L. M., Zulueta J., Nadal E., Rosell A., Esteller M., Sandoval J. A novel epigenetic signature for early diagnosis in lung cancer. Clinical Cancer Research, 2016, vol. 22, no. 13, pp. 3361–3371. https://doi.org/10.1158/1078-0432.ccr-15-2346

4. Detilleux D., Spill Y. G., Balaramane D., Weber M., Bardet A. F. Pan-cancer predictions of transcription factors mediating aberrant DNA methyl ation. Epigenetics and Chromatin, 2022, vol. 15, no. 1. https://doi.org/10.1186/s13072-022-00443-w

5. Fukushige S., Horii A. DNA methylation in cancer: a gene silencing mechanism and the clinical potential of its biomarkers. Tohoku Journal of Experimental Medicine, 2013, vol. 229, no. 3, pp. 173–185. https://doi.org/10.1620/tjem.229.173

6. Laplana M., Bieg M., Faltus C., Melnik S., Bogatyrova O., Gu Z., Muley T., Meister M., Dienemann H., Herpel E., Amos C. I., Schlesner M., Eils R., Plass C., Risch A. Differentially methylated regions within lung cancer risk loci are enriched in deregulated enhancers. Epigenetics, 2021, vol. 17, no. 2, pp. 117–132. https://doi.org/10.1080/15592294.2021.1878723

7. Yang B., Bhusari S., Kueck J., Weeratunga P., Wagner J., Leverson G., Huang W., Jarrard D. F. Methylation profiling defines an extensive field defect in histologically normal prostate tissues associated with prostate cancer. Neoplasia, 2013, vol. 15, no. 4, pp. 399–408. https://doi.org/10.1593/neo.13280

8. Ooki A., Maleki Z., Tsay J.-C. J., Goparaju Ch., Brait M., Turaga N., Nam H.-S., Rom W. N., Pass H. I., Sidransky D., Guerrero-Preston R., Hoque M. O. A Panel of Novel Detection and Prognostic Methylated DNA Markers in Primary Non– Small Cell Lung Cancer and Serum DNA. Clinical Cancer Research, 2017, vol. 23, no. 22, pp. 7141–7152. https://doi.org/10.1158/1078-0432.ccr-17-1222

9. Zhao N., Ruan M., Koestler D. C., Lu J., Marsit C. J., Kelsey K. T., Platz E. A., Michaud D. S. Epigenome-wide scan identifies differentially methylated regions for lung cancer using pre-diagnostic peripheral blood. Epigenetics, 2022, vol. 17, no. 4, pp. 460–472. https://doi.org/10.1080/15592294.2021.1923615

10. Huang Yi, Yu Z., Zheng M., Yang X., Huang H., Zhao L. Methylation-associated inactivation of JPH3 and its effect on prognosis and cell biological function in HCC. Molecular Medicine Reports, 2022, vol. 25, no. 4, art. 124. https://doi.org/10.3892/mmr.2022.12640

11. Kalmár A., Péterfia B., Hollósi P., Galamb O., Spisák S., Wichmann B., Bodor A., Tóth K., Patai Á. V., Valcz G., Nagy Z. B., Kubák V., Tulassay Z., Kovalszky I., Molnár B. DNA hypermethylation and decreased mRNA expression of MAL, PRIMA1, PTGDR and SFRP1 in colorectal adenoma and cancer. BioMed Central Cancer, 2015, vol. 15, no. 1, art. 736. https://doi.org/10.1186/s12885-015-1687-x

12. Pradhan M. P., Desai A., Palakal M. J. Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma. BMC Systems Biology, 2013, vol. 7, no. 1, art. 141. https://doi.org/10.1186/1752-0509-7-141

13. Daniele G., Simonetti G., Fusilli C., Iacobucci I., Lonoce A., Palazzo A., Lomiento M. [et al.]. Epigenetically induced ectopic expression of UNCX impairs the proliferation and differentiation of myeloid cells. Haematologica, 2017, vol. 102, no. 7, pp. 1204–1214. https://doi.org/10.3324/haematol.2016.163022

14. Cai H., Ke Z. B., Dong R. N., Chen H., Lin F., Zheng W. C., Chen S. H., Zhu J. M., Chen S. M., Zheng Q. S., Wei Y., Xue X. Y., Xu N. The prognostic value of homeobox A9 (HOXA9) methylation in solid tumors: a systematic review and metaanalysis. Translation Cancer Research, 2021, vol. 10, no. 10, pp. 4347–4354. https://doi.org/10.21037/tcr-21-765

15. Kitchen M. O., Bryan R. T., Haworth K. E., Emes R. D., Luscombe Ch., Gommersall L., Cheng K. K., Zeegers M. P., James N. D., Devall A. J., Fryer A. A., Farrell W. E. Methylation of HOXA9 and ISL1 Predicts Patient Outcome in HighGrade Non-Invasive Bladder Cancer. PLoS One, 2015, vol. 10, no. 9, art. e0137003. https://doi.org/10.1371/journal.pone.0137003