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Promoter hypermethylation of GALR1 acts as an early epigenetic susceptibility event in colorectal carcinogenesis

Abstract

Epigenetics play an essential role in colorectal neoplasia process. There is a need to determine the appropriateness of epigenetic biomarkers for early detection as well as expand our understanding of the carcinogenic process. Therefore, the aim of the study was to assess how DNA methylation pattern of GALR1 gene evolves in a sample set representing colorectal neoplastic progression. The study was designed into three phases. Firstly, Methylation status of GALR1 was assessed with genome-wide DNA methylation beadchip and pyrosequencing assays in colorectal lesions and paired normal tissues. Then, linear mixed-effects modeling analyses were applied to describe the trend of DNA methylation during the progression of colorectal neoplasia. In the third phase, quantitative RT-PCR was used to examine GALR1 expression in patients with precursor lesion and colorectal cancer. We found that significant hypermethylation of GALR1 promoter was a widely existent modification in CRCs (P < 0.001). When further examined methylation pattern of GALR1 during neoplastic progression of CRC, we found that DNA methylation level of GALR1 showed a significant stepwise increase from normal to hyperplastic polyps, to adenomas and to carcinoma samples (P < 0.001). Besides, loss of mRNA expression is a common accompaniment to adenomas and carcinomas. Public omics data analyses showed an inverse correlation between gene expression and DNA methylation (P < 0.001). Our findings indicate that epigenetic alteration of GALR1 promoter is gradually accumulated during the colorectal neoplastic progression. It can potentially be a promising biomarker used for screening and surveillance of colorectal cancer.

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References

  1. Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68:394–424.

    PubMed  Article  Google Scholar 

  2. Day DW, Morson BC. The adenoma-carcinoma sequence. Major Probl Pathol. 1978;10:58–71.

    CAS  PubMed  Google Scholar 

  3. Vogelstein B, Fearon ER, Hamilton SR, Kern SE, Preisinger AC, Leppert M, et al. Genetic alterations during colorectal-tumor development. N Engl J Med. 1988;319:525–32.

    CAS  PubMed  Article  Google Scholar 

  4. Sharma S, Kelly TK, Jones PA. Epigenetics in cancer. Carcinogenesis. 2010;31:27–36.

    CAS  PubMed  Article  Google Scholar 

  5. Lakshminarasimhan R, Liang G. The role of DNA methylation in cancer. Adv Exp Med Biol. 2016;945:151–72.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  6. Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet. 2006;7:21–33.

    CAS  PubMed  Article  Google Scholar 

  7. Kulis M, Esteller M. DNA methylation and cancer. Adv Genet. 2010;70:27–56.

    PubMed  Article  Google Scholar 

  8. Sina AA, Carrascosa LG, Liang Z, Grewal YS, Wardiana A, Shiddiky M, et al. Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker. Nat Commun. 2018;9:4915.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  9. Eden A, Gaudet F, Waghmare A, Jaenisch R. Chromosomal instability and tumors promoted by DNA hypomethylation. Science. 2003;300:455.

    CAS  PubMed  Article  Google Scholar 

  10. Pfeifer GP. Defining driver DNA methylation changes in human cancer. Int J Mol Sci. 2018;19:1166.

  11. Ogino S, Nosho K, Kirkner GJ, Kawasaki T, Chan AT, Schernhammer ES, et al. A cohort study of tumoral LINE-1 hypomethylation and prognosis in colon cancer. J Natl Cancer Inst. 2008;100:1734–8.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. Yoshiura K, Kanai Y, Ochiai A, Shimoyama Y, Sugimura T, Hirohashi S. Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas. Proc Natl Acad Sci USA. 1995;92:7416–9.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  13. Herman JG, Merlo A, Mao L, Lapidus RG, Issa JP, Davidson NE, et al. Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers. Cancer Res. 1995;55:4525–30.

    CAS  PubMed  Google Scholar 

  14. Kane MF, Loda M, Gaida GM, Lipman J, Mishra R, Goldman H, et al. Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res. 1997;57:808–11.

    CAS  PubMed  Google Scholar 

  15. Bai AH, Tong JH, To KF, Chan MW, Man EP, Lo KW, et al. Promoter hypermethylation of tumor-related genes in the progression of colorectal neoplasia. Int J Cancer. 2004;112:846–53.

    CAS  PubMed  Article  Google Scholar 

  16. Luo Y, Wong CJ, Kaz AM, Dzieciatkowski S, Carter KT, Morris SM, et al. Differences in DNA methylation signatures reveal multiple pathways of progression from adenoma to colorectal cancer. Gastroenterology. 2014;147:418–29.

    CAS  PubMed  Article  Google Scholar 

  17. Habert-Ortoli E, Amiranoff B, Loquet I, Laburthe M, Mayaux JF. Molecular cloning of a functional human galanin receptor. Proc Natl Acad Sci USA. 1994;91:9780–3.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  18. Webling KE, Runesson J, Bartfai T, Langel U. Galanin receptors and ligands. Front Endocrinol (Lausanne). 2012;3:146.

    Article  Google Scholar 

  19. Stevenson L, Allen WL, Turkington R, Jithesh PV, Proutski I, Stewart G, et al. Identification of galanin and its receptor GAlR1 as novel determinants of resistance to chemotherapy and potential biomarkers in colorectal cancer. Clin Cancer Res. 2012;18:5412–26.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  20. Rauch I, Kofler B. The galanin system in cancer. Exp Suppl. 2010;102:223–41.

    CAS  PubMed  Google Scholar 

  21. Lappano R, Maggiolini M. G protein-coupled receptors: novel targets for drug discovery in cancer. Nat Rev Drug Disco. 2011;10:47–60.

    CAS  Article  Google Scholar 

  22. Gu S, Lin S, Ye D, Qian S, Jiang D, Zhang X, et al. Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer. Clin Epigenetics. 2019;11:41.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  23. Chen K, Jin M, Zhu Y, Jiang Q, Yu W, Ma X, et al. Genetic polymorphisms of the uridine diphosphate glucuronosyltransferase 1a7 and colorectal cancer risk in relation to cigarette smoking and alcohol drinking in a chinese population. J Gastroenterol Hepatol. 2006;21:1036–41.

    CAS  PubMed  Article  Google Scholar 

  24. Jin M, Gu S, Ye D, Li Y, Jing F, Li Q, et al. Association between genetic variants in the promoter region of a novel antisense long noncoding RNA RP11-392P7.6 and colorectal cancer risk. Environ Mol Mutagen. 2017;58:434–42.

    CAS  PubMed  Article  Google Scholar 

  25. Wang D, Yan L, Hu Q, Sucheston LE, Higgins MJ, Ambrosone CB, et al. IMA: an R package for high-throughput analysis of illumina’s 450K infinium methylation data. Bioinformatics. 2012;28:729–30.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  26. Curtius K, Wright NA, Graham TA. An evolutionary perspective on field cancerization. Nat Rev Cancer. 2018;18:19–32.

    CAS  PubMed  Article  Google Scholar 

  27. Ibrahim AE, Arends MJ, Silva AL, Wyllie AH, Greger L, Ito Y, et al. Sequential DNA methylation changes are associated with DNMT3B overexpression in colorectal neoplastic progression. Gut. 2011;60:499–508.

    CAS  PubMed  Article  Google Scholar 

  28. Ding W, Chen J, Feng G, Chen G, Wu J, Guo Y, et al. DNMIVD: DNA methylation interactive visualization database. Nucleic Acids Res. 2020;48:D856–62.

    CAS  PubMed  Article  Google Scholar 

  29. Misawa K, Ueda Y, Kanazawa T, Misawa Y, Jang I, Brenner JC, et al. Epigenetic inactivation of galanin receptor 1 in head and neck cancer. Clin Cancer Res. 2008;14:7604–13.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  30. Knösel T, Petersen S, Schwabe H, Schlüns K, Stein U, Schlag PM, et al. Incidence of chromosomal imbalances in advanced colorectal carcinomas and their metastases. Virchows Arch. 2002;440:187–94.

    PubMed  Article  CAS  Google Scholar 

  31. Lang R, Gundlach AL, Kofler B. The galanin peptide family: receptor pharmacology, pleiotropic biological actions, and implications in health and disease. Pharm Ther. 2007;115:177–207.

    CAS  Article  Google Scholar 

  32. Kanazawa T, Iwashita T, Kommareddi P, Nair T, Misawa K, Misawa Y, et al. Galanin and galanin receptor type 1 suppress proliferation in squamous carcinoma cells: activation of the extracellular signal regulated kinase pathway and induction of cyclin-dependent kinase inhibitors. Oncogene.2007;26:5762–71.

    CAS  PubMed  Article  Google Scholar 

  33. Henson BS, Neubig RR, Jang I, Ogawa T, Zhang Z, Carey TE, et al. Galanin receptor 1 has anti-proliferative effects in oral squamous cell carcinoma. J Biol Chem. 2005;280:22564–71.

    CAS  PubMed  Article  Google Scholar 

  34. Misawa K, Misawa Y, Kanazawa T, Mochizuki D, Imai A, Endo S, et al. Epigenetic inactivation of galanin and GALR1/2 is associated with early recurrence in head and neck cancer. Clin Exp Metastasis. 2016;33:187–95.

    CAS  PubMed  Article  Google Scholar 

  35. Guo S, Yan F, Xu J, Bao Y, Zhu J, Wang X, et al. Identification and validation of the methylation biomarkers of non-small cell lung cancer (NSCLC). Clin Epigenetics. 2015;7:3.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  36. Kanazawa T, Misawa K, Fukushima H, Misawa Y, Sato Y, Maruta M, et al. Epigenetic inactivation of galanin receptors in salivary duct carcinoma of the parotid gland: potential utility as biomarkers for prognosis. Oncol Lett. 2018;15:9043–50.

    PubMed  PubMed Central  Google Scholar 

  37. Doufekas K, Hadwin R, Kandimalla R, Jones A, Mould T, Crowe S, et al. Galr1 methylation in vaginal swabs is highly accurate in identifying women with endometrial cancer. Int J Gynecol Cancer. 2013;23:1050–5.

    PubMed  Article  Google Scholar 

  38. Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 2008;9:465–76.

    CAS  PubMed  Article  Google Scholar 

  39. Zhu H, Wang G, Qian J. Transcription factors as readers and effectors of DNA methylation. Nat Rev Genet. 2016;17:551–65.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  40. Bird AP, Wolffe AP. Methylation-induced repression-belts, braces, and chromatin. Cell. 1999;99:451–4.

    CAS  PubMed  Article  Google Scholar 

  41. Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E. Swissregulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res. 2013;41:D214–20.

    CAS  PubMed  Article  Google Scholar 

  42. Kim SH, Park YY, Cho SN, Margalit O, Wang D, DuBois RN. Krüppel-like factor 12 promotes colorectal cancer growth through early growth response protein 1. Plos ONE. 2016;11:e159899.

    Google Scholar 

  43. Shen A, Chen Y, Liu L, Huang Y, Chen H, Qi F, et al. EBF1-mediated upregulation of ribosome assembly factor PON1 contributes to cancer progression by negatively regulating the p53 signaling pathway. Cancer Res. 2019;79:2257–70.

    CAS  PubMed  Article  Google Scholar 

  44. Slaughter DP, Southwick HW, Smejkal W. Field cancerization in oral stratified squamous epithelium; Clinical implications of multicentric origin. Cancer. 1953;6:963–8.

    CAS  PubMed  Article  Google Scholar 

  45. Lochhead P, Chan AT, Nishihara R, Fuchs CS, Beck AH, Giovannucci E, et al. Etiologic field effect: reappraisal of the field effect concept in cancer predisposition and progression. Mod Pathol. 2015;28:14–29.

    PubMed  Article  Google Scholar 

  46. Ando T, Yoshida T, Enomoto S, Asada K, Tatematsu M, Ichinose M, et al. DNA methylation of microRNA genes in gastric mucosae of gastric cancer patients: its possible involvement in the formation of epigenetic field defect. Int J Cancer. 2009;124:2367–74.

    CAS  PubMed  Article  Google Scholar 

  47. Jin Z, Zhao Z, Cheng Y, Dong M, Zhang X, Wang L, et al. Endoglin promoter hypermethylation identifies a field defect in human primary esophageal cancer. Cancer. 2013;119:3604–9.

    CAS  PubMed  Article  Google Scholar 

  48. Koizumi K, Alonso S, Miyaki Y, Okada S, Ogura H, Shiiya N, et al. Array-based identification of common DNA methylation alterations in ulcerative colitis. Int J Oncol. 2012;40:983–94.

    CAS  PubMed  Article  Google Scholar 

  49. Oberg AL, Mahoney DW. Linear mixed effects models. Methods Mol Biol. 2007;404:213–34.

    PubMed  Article  Google Scholar 

  50. Wanichthanarak K, Jeamsripong S, Pornputtapong N, Khoomrung S. Accounting for biological variation with linear mixed-effects modelling improves the quality of clinical metabolomics data. Comput Struct Biotechnol J. 2019;17:611–8.

    PubMed  PubMed Central  Article  Google Scholar 

  51. Grady WM. Epigenetic events in the colorectum and in colon cancer. Biochem Soc Trans. 2005;33:684–8.

    CAS  PubMed  Article  Google Scholar 

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Acknowledgements

We sincerely thank all participants in the study.

Funding

This study is supported by National Basic Research Program of China (973 Program No.2015CB554003), National Science Foundation of China (NSFC No.81673262) and Zhejiang Provincial Natural Science Foundation of China (Q22H260581).

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SG and MJ designed and supervised the whole study. SG, SQ and SL performed the experiments. SG and DY made contributions to statistical analyses. QL, JY, XY, ZL, MT and JW recruited the participants and collected samples and clinical information. SG completed the manuscript with intellectual input from MJ and KC. All authors read and approved the final manuscript.

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Correspondence to Kun Chen or Mingjuan Jin.

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The study was conducted according to the guidelines of the Declaration of Helsinki, and approved by Ethics Committee of Zhejiang University School of Medicine. The patients/participants provided their written informed consent to participate in this study.

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Gu, S., Qian, S., Lin, S. et al. Promoter hypermethylation of GALR1 acts as an early epigenetic susceptibility event in colorectal carcinogenesis. J Hum Genet 67, 519–525 (2022). https://doi.org/10.1038/s10038-022-01038-9

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