Research Article

Epigenetic signature discriminates lymphatic metastasis in BRAF wild-type thyroid carcinoma: methylation role of GRIK2

https://orcid.org/0009-0002-2084-5855

State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China

‡These authors contributed equally to this work

Search for more papers by this author

Qingfeng Zhang‡

State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China

‡These authors contributed equally to this work

Search for more papers by this author

Fei Lin‡

Department of Oncology, Guangdong Provincial Hospital of Integrated Traditional Chinese & Western Medicine, Affiliated Nanhai Hospital of Traditional Chinese Medicine of Jinan University, Foshan, Guangdong Province, 528200, China

‡These authors contributed equally to this work

Search for more papers by this author

Chao Ke

State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China

Search for more papers by this author

Wuguo Deng

State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China

Search for more papers by this author

Ankui Yang

State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China

Search for more papers by this author

Xuan Su

*Author for correspondence:

E-mail Address: michaelsu87@sina.com

https://orcid.org/0000-0002-8963-2519

State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China

Search for more papers by this author

Published Online:22 Nov 2023https://doi.org/10.2217/epi-2023-0334

View article

Abstract

Aim: Conservative treatment approaches for thyroid carcinoma (TC) patients with wild-type B-type Raf kinase (BRAF) pose risks of long-term recurrence. The association of DNA methylation with TC metastasis is unclear. Patients & methods: Here we analyzed data from 179 BRAF wild-type TC patients in the The Cancer Genome Atlas database, identifying significant metastasis-associated CpGs. A logistic regression model was developed and validated for discriminating lymphatic metastasis in BRAF wild-type TC. Results: The model showed high accuracy (AUC: 0.924 training set; 0.812 and 0.773 external cohorts). TAGLN, MRPL4, CLDN10 and GRIK2 emerged as diagnostic markers. GRIK2, downregulated due to promoter hypermethylation, acted as a TC suppressor. Conclusion: Our 5-CpG epigenetic signature effectively discriminates lymphatic metastasis in BRAF wild-type TC, highlighting GRIK2‘s tumor-suppressive role influenced by promoter hypermethylation.

Keywords:

Papers of special note have been highlighted as: • of interest; •• of considerable interest

References

1. Sung H, Ferlay J, Siegel RL et al. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. Cancer J. Clin. 71(3), 209–249 (2021).
MedlineGoogle Scholar
2. Siegel RL, Miller KD, Jemal A. Cancer statistics, 2020. Cancer J. Clin. 70(1), 7–30 (2020).
MedlineGoogle Scholar
3. Davies L, Morris LG, Haymart M et al. American association of clinical endocrinologists and american college of endocrinology disease state clinical review: the increasing incidence of thyroid cancer. Endocrine Pract. 21(6), 686–696 (2015).
MedlineGoogle Scholar
4. Hundahl SA, Fleming ID, Fremgen AM, Menck HR. A National Cancer Data Base report on 53,856 cases of thyroid carcinoma treated in the U.S., 1985–1995 [see commetns]. Cancer 83(12), 2638–2648 (1998).
Medline CASGoogle Scholar
5. Döbert N, Menzel C, Oeschger S, Grünwald F. Differentiated thyroid carcinoma: the new UICC 6th edition TNM classification system in a retrospective analysis of 169 patients. Thyroid 14(1), 65–70 (2004).
MedlineGoogle Scholar
6. Francis GL, Waguespack SG, Bauer AJ et al. Management Guidelines for Children with Thyroid Nodules and Differentiated Thyroid Cancer. Thyroid 25(7), 716–759 (2015).
MedlineGoogle Scholar
7. Loh KC, Greenspan FS, Gee L, Miller TR, Yeo PP. Pathological tumor-node-metastasis (pTNM) staging for papillary and follicular thyroid carcinomas: a retrospective analysis of 700 patients. J. Clin. Endocrinol. Metabol. 82(11), 3553–3562 (1997).
Medline CASGoogle Scholar
8. Kitamura Y, Shimizu K, Nagahama M et al. Immediate causes of death in thyroid carcinoma: clinicopathological analysis of 161 fatal cases. J. Clin. Endocrinol. Metabol. 84(11), 4043–4049 (1999).
Medline CASGoogle Scholar
9. Lupi C, Giannini R, Ugolini C et al. Association of BRAF V600E mutation with poor clinicopathological outcomes in 500 consecutive cases of papillary thyroid carcinoma. J. Clin. Endocrinol. Metabol. 92(11), 4085–4090 (2007).
Medline CASGoogle Scholar
10. Trovisco V, Soares P, Preto A et al. Type and prevalence of BRAF mutations are closely associated with papillary thyroid carcinoma histotype and patients’ age but not with tumour aggressiveness. Virchows Arch. 446(6), 589–595 (2005).
Medline CASGoogle Scholar
11. Frasca F, Nucera C, Pellegriti G et al. BRAF(V600E) mutation and the biology of papillary thyroid cancer. Endocr. Relat. Cancer 15(1), 191–205 (2008).
Medline CASGoogle Scholar
12. Tang KT, Lee CH. BRAF mutation in papillary thyroid carcinoma: pathogenic role and clinical implications. JCMA 73(3), 113–128 (2010).
CASGoogle Scholar
13. Kim TH, Park YJ, Lim JA et al. The association of the BRAF(V600E) mutation with prognostic factors and poor clinical outcome in papillary thyroid cancer: a meta-analysis. Cancer 118(7), 1764–1773 (2012).
Medline CASGoogle Scholar
14. Tao Y, Wang F, Shen X et al. BRAF V600E status sharply differentiates lymph node metastasis-associated mortality risk in papillary thyroid cancer. J. Clin. Endocrinol. Metabol. 106(11), 3228–3238 (2021).
MedlineGoogle Scholar
15. Das PM, Singal R. DNA methylation and cancer. J. Clin. Oncol. 22(22), 4632–4642 (2004).
Medline CASGoogle Scholar
16. Klutstein M, Nejman D, Greenfield R, Cedar H. DNA methylation in cancer and aging. Cancer Res. 76(12), 3446–3450 (2016).
Medline CASGoogle Scholar
17. Jensen K, Patel A, Hoperia V, Larin A, Bauer A, Vasko V. Dynamic changes in E-cadherin gene promoter methylation during metastatic progression in papillary thyroid cancer. Exp. Ther. Med. 1(3), 457–462 (2010). • Establishes that the dynamic changes in gene promoter methylation do indeed regulate the process of metastasis in thyroid carcinoma.
Medline CASGoogle Scholar
18. Wang P, Pei R, Lu Z, Rao X, Liu B. Methylation of p16 CpG islands correlated with metastasis and aggressiveness in papillary thyroid carcinoma. JCMA 76(3), 135–139 (2013).
CASGoogle Scholar
19. Tomczak K, Czerwińska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp. Oncol. (Poznan, Poland) 19(1a), A68–A77 (2015).
MedlineGoogle Scholar
20. Beltrami CM, Dos Reis MB, Barros-Filho MC et al. Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas. Clin. Epigenetics 9, 45 (2017).
MedlineGoogle Scholar
21. Bisarro Dos Reis M, Barros-Filho MC, Marchi FA et al. Prognostic classifier based on genome-wide DNA methylation profiling in well-differentiated thyroid tumors. J. Clin. Endocrinol. Metabol. 102(11), 4089–4099 (2017).
MedlineGoogle Scholar
22. Shiny Methylation Analysis Resource Tool (SMART). www.bioinfo-zs.com/smartapp/
Google Scholar
23. UCSC Genomics Institute.Genome Browser. http://genome.ucsc.edu/
Google Scholar
24. MethPrimer 2.0. www.urogene.org/methprimer2/
Google Scholar
25. Pellegriti G, Frasca F, Regalbuto C, Squatrito S, Vigneri R. Worldwide increasing incidence of thyroid cancer: update on epidemiology and risk factors. J. Cancer Epidemiol. 2013, 965212 (2013).
MedlineGoogle Scholar
26. Kitahara CM, Sosa JA. The changing incidence of thyroid cancer. Nat. Rev. Endocrinol. 12(11), 646–653 (2016).
MedlineGoogle Scholar
27. Mazzaferri EL, Jhiang SM. Long-term impact of initial surgical and medical therapy on papillary and follicular thyroid cancer. Am. J. Med. 97(5), 418–428 (1994).
Medline CASGoogle Scholar
28. Sakorafas GH, Sampanis D, Safioleas M. Cervical lymph node dissection in papillary thyroid cancer: current trends, persisting controversies, and unclarified uncertainties. Surg. Oncol. 19(2), e57–e70 (2010). •• Highlights the importance of accurately identifying lymphatic metastasis prior to thyroid carcinoma surgery for effective surgical planning.
MedlineGoogle Scholar
29. Wu B-K, Mei S-C, Chen EH, Zheng Y, Pan D. YAP induces an oncogenic transcriptional program through TET1-mediated epigenetic remodeling in liver growth and tumorigenesis. Nat. Genet. 54(8), 1202–1213 (2022).
MedlineGoogle Scholar
30. Zhu X, Xue C, Kang X et al. DNMT3B-mediated FAM111B methylation promotes papillary thyroid tumor glycolysis, growth and metastasis. Int. J. Biol. Sci. 18(11), 4372–4387 (2022). • Demonstrates that DNMT3b-mediated oncogene promoter methylation plays a critical role in the development and progression of thyroid carcinoma.
Medline CASGoogle Scholar
31. Ahn HR, Baek GO, Yoon MG et al. Hypomethylation-mediated upregulation of the WASF2 promoter region correlates with poor clinical outcomes in hepatocellular carcinoma. J. Exp. Clin. Cancer Res. 41(1), 158 (2022).
Medline CASGoogle Scholar
32. Sun D, Gan X, Liu L et al. DNA hypermethylation modification promotes the development of hepatocellular carcinoma by depressing the tumor suppressor gene ZNF334. Cell Death Dis. 13(5), 446 (2022). • Reveals that hypermethylation in the promoter region of tumor-suppressor genes in liver cancer contributes to tumor progression.
Medline CASGoogle Scholar
33. Puxeddu E, Durante C, Avenia N, Filetti S, Russo D. Clinical implications of BRAF mutation in thyroid carcinoma. Trends Endocrinol. Metab. 19(4), 138–145 (2008).
Medline CASGoogle Scholar
34. Dvorakova M, Nenutil R, Bouchal P. Transgelins, cytoskeletal proteins implicated in different aspects of cancer development. Expert Rev. Proteomics 11(2), 149–165 (2014).
Medline CASGoogle Scholar
35. Wei X, Lou H, Zhou D et al. TAGLN mediated stiffness-regulated ovarian cancer progression via RhoA/ROCK pathway. J. Exp. Clin. Cancer Res. 40(1), 292 (2021).
Medline CASGoogle Scholar
36. Chen Z, He S, Zhan Y et al. TGF-β-induced transgelin promotes bladder cancer metastasis by regulating epithelial-mesenchymal transition and invadopodia formation. EBioMedicine 47, 208–220 (2019).
MedlineGoogle Scholar
37. Lin X, Guo L, Lin X, Wang Y, Zhang G. Expression and prognosis analysis of mitochondrial ribosomal protein family in breast cancer. Sci. Rep. 12(1), 10658 (2022).
Medline CASGoogle Scholar
38. Xiang Z, Zhong C, Chang A et al. Immune-related key gene CLDN10 correlates with lymph node metastasis but predicts favorable prognosis in papillary thyroid carcinoma. Aging 12(3), 2825–2839 (2020). • Demonstrates that high expression of CLDN10 is closely associated with lymphatic metastasis in papillary thyroid carcinoma, but also improves prognosis by promoting increased lymphocyte infiltration.
Medline CASGoogle Scholar
39. Yang W, Zhang K, Zhang Z et al. Claudin-10 overexpression suppresses human clear cell renal cell carcinoma growth and metastasis by regulating ATP5O and causing mitochondrial dysfunction. Int. J. Biol. Sci. 18(6), 2329–2344 (2022).
Medline CASGoogle Scholar
40. Huang J, Teng L, Liu T et al. Identification of a novel serine/threonine kinase that inhibits TNF-induced NF-κB activation and p53-induced transcription. Biochem. Biophys. Res. Comm. 309(4), 774–778 (2003).
Medline CASGoogle Scholar
41. Paschen W, Blackstone CD, Huganir RL, Ross CA. Human GluR6 kainate receptor (GRIK2): molecular cloning, expression, polymorphism, and chromosomal assignment. Genomics 20(3), 435–440 (1994).
Medline CASGoogle Scholar
42. Barbon A, Vallini I, Barlati S. Genomic organization of the human GRIK2 gene and evidence for multiple splicing variants. Gene 274(1–2), 187–197 (2001).
Medline CASGoogle Scholar
43. Zhawar VK, Kaur G, Deriel JK, Kaur GP, Kandpal RP, Athwal RS. Novel spliced variants of ionotropic glutamate receptor GluR6 in normal human fibroblast and brain cells are transcribed by tissue specific promoters. Gene 459(1–2), 1–10 (2010).
Medline CASGoogle Scholar
44. Wu CS, Lu YJ, Li HP et al. Glutamate receptor, ionotropic, kainate 2 silencing by DNA hypermethylation possesses tumor suppressor function in gastric cancer. Int. J. Cancer 126(11), 2542–2552 (2010).
Medline CASGoogle Scholar
45. Zhawar VK, Kandpal RP, Athwal RS. Isoforms of Ionotropic Glutamate Receptor GRIK2 Induce Senescence of Carcinoma Cells. Cancer Genom. Proteom. 16(1), 59–64 (2019).
Medline CASGoogle Scholar
46. Zhawar VK, Kandpal RP, Athwal RS. Alternative promoters of GRIK2 (GluR6) gene in human carcinoma cell lines are regulated by differential methylation of CpG dinucleotides. Genes (Basel) 13(3), 493 (2022). •• Demonstrates that transcriptional variants of GRIK2, resulting from differential promoter methylation, may contribute to the development of distinct characteristics in tumor cells.
MedlineGoogle Scholar
47. Wade PA, Gegonne A, Jones PL, Ballestar E, Aubry F, Wolffe AP. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat. Genet. 23(1), 62–66 (1999).
Medline CASGoogle Scholar

Vol. 15, No. 21

Supplemental Materials

Metrics

Downloaded 44 times

History

Received 23 September 2023

Accepted 9 November 2023

Published online 22 November 2023

Published in print November 2023

Information

Keywords

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.futuremedicine.com/doi/suppl/10.2217/epi-2023-0334

Author contributions

J Peng, Q Zhang and F Lin contributed equally and share the first authorship. J Peng, Q Zhang, A Yang and X Su. conceived and designed the project. J Peng, Q Zhang, C Ke, W Deng, F Lin and X Su. performed the experiments and analyzed and interpreted the data. J Peng, Q Zhang, W Deng, F Lin and X Su. wrote and revised the manuscript. All authors read and approved the final manuscript.

Acknowledgments

The authors thank all members of W Deng's 727 laboratory and A Yang's 833 Laboratory for their advice and technical assistance.

Financial disclosure

This work was supported by the funds from the National Natural Science Foundation of China (82072981, 82272649), Natural Science Foundation of Guangdong Province (2019A1515010150) and Guangdong Basic and Applied Basic Research Foundation (2021A1515010083). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Competing interests disclosure

The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Writing disclosure

No writing assistance was utilized in the production of this manuscript.

Ethical disclosure

Clinical samples were obtained from the Tumor Bio-bank of Sun Yat-sen University Cancer Center. The study protocol for the SYSUCC cohort was approved by the Institutional Research Ethics Committee of Sun Yat-sen University Cancer Center (B2023-169-01). In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Data sharing statement

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Materials.

PDF download