Genome wide DNA methylation profiling identifies specific epigenetic features in high-risk cutaneous squamous cell carcinoma

Autoři: David Hervás-Marín aff001;  Faatiemah Higgins aff002;  Onofre Sanmartín aff004;  Jose Antonio López-Guerrero aff006;  M. Carmen Bañó aff002;  J. Carlos Igual aff002;  Inma Quilis aff002;  Juan Sandoval aff007
Působiště autorů: Department of Biostatistics, Instituto de Investigación Sanitaria La Fe, Valencia, Spain aff001;  Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) Universitat de València, Burjassot, Valencia, Spain aff002;  Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Valencia, Spain aff003;  Dermatology Department, Instituto Valenciano de Oncología, Valencia, Spain aff004;  Facultad de Medicina, Universidad Católica de Valencia, Valencia, Spain aff005;  Laboratory of Molecular Biology, Instituto Valenciano de Oncología, Valencia, Spain aff006;  Biomarkers and Precision Medicine Unit (UByMP), Instituto de Investigación Sanitaria La Fe, Valencia, Spain aff007
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article


Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. Although most cSCCs have good prognosis, a subgroup of high-risk cSCC has a higher frequency of recurrence and mortality. Therefore, the identification of molecular risk factors associated with this aggressive subtype is of major interest. In this work we carried out a global-scale approach to investigate the DNA-methylation profile in patients at different stages, from premalignant actinic keratosis to low-risk invasive and high-risk non-metastatic and metastatic cSCC. The results showed massive non-sequential changes in DNA-methylome and identified a minimal methylation signature that discriminates between stages. Importantly, a direct comparison of low-risk and high-risk stages revealed epigenetic traits characteristic of high-risk tumours. Finally, a prognostic prediction model in cSCC patients identified a methylation signature able to predict the overall survival of patients. Thus, the analysis of DNA-methylation in cSCC revealed changes during the evolution of the disease through the different stages that can be of great value not only in the diagnosis but also in the prognosis of the disease.

Klíčová slova:

Cancer detection and diagnosis – Carcinomas – DNA methylation – Epigenetics – Prognosis – Squamous cell carcinomas – Treatment guidelines – Actinic keratosis


1. Donaldson MR, Coldiron BM. No en d in sight: the skin cancer epidemic continues. Semin Cutan Med Surg. 2011;30(1):3–5. doi: 10.1016/j.sder.2011.01.002 21540015.

2. Alam M, Ratner D. Cutaneous squamous-cell carcinoma. N Engl J Med. 2001;344(13):975–83. doi: 10.1056/NEJM200103293441306 11274625.

3. Green AC, Olsen CM. Cutaneous squamous cell carcinoma: an epidemiological review. Br J Dermatol. 2017;177(2):373–81. doi: 10.1111/bjd.15324 28211039.

4. Leiter U, Keim U, Eigentler T, Katalinic A, Holleczek B, Martus P, et al. Incidence, Mortality, and Trends of Nonmelanoma Skin Cancer in Germany. J Invest Dermatol. 2017;137(9):1860–7. doi: 10.1016/j.jid.2017.04.020 28487088.

5. Schmults CD, Karia PS, Carter JB, Han J, Qureshi AA. Factors predictive of recurrence and death from cutaneous squamous cell carcinoma: a 10-year, single-institution cohort study. JAMA Dermatol. 2013;149(5):541–7. doi: 10.1001/jamadermatol.2013.2139 23677079.

6. Ruiz ES, Karia PS, Besaw R, Schmults CD. Performance of the American Joint Committee on Cancer Staging Manual, 8th Edition vs the Brigham and Women's Hospital Tumor Classification System for Cutaneous Squamous Cell Carcinoma. JAMA Dermatol. 2019. doi: 10.1001/jamadermatol.2019.0032 30969315.

7. Inman GJ, Wang J, Nagano A, Alexandrov LB, Purdie KJ, Taylor RG, et al. The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature. Nat Commun. 2018;9(1):3667. doi: 10.1038/s41467-018-06027-1 30202019; PubMed Central PMCID: PMC6131170.

8. Pickering CR, Zhou JH, Lee JJ, Drummond JA, Peng SA, Saade RE, et al. Mutational landscape of aggressive cutaneous squamous cell carcinoma. Clin Cancer Res. 2014;20(24):6582–92. doi: 10.1158/1078-0432.CCR-14-1768 25303977; PubMed Central PMCID: PMC4367811.

9. South AP, Purdie KJ, Watt SA, Haldenby S, den Breems N, Dimon M, et al. NOTCH1 mutations occur early during cutaneous squamous cell carcinogenesis. J Invest Dermatol. 2014;134(10):2630–8. doi: 10.1038/jid.2014.154 24662767; PubMed Central PMCID: PMC4753672.

10. Harwood CA, Proby CM, Inman GJ, Leigh IM. The Promise of Genomics and the Development of Targeted Therapies for Cutaneous Squamous Cell Carcinoma. Acta Derm Venereol. 2016;96(1):3–16. doi: 10.2340/00015555-2181 26084328.

11. Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA, et al. Temporal dissection of tumorigenesis in primary cancers. Cancer Discov. 2011;1(2):137–43. doi: 10.1158/2159-8290.CD-11-0028 21984974; PubMed Central PMCID: PMC3187561.

12. Giglia-Mari G, Sarasin A. TP53 mutations in human skin cancers. Hum Mutat. 2003;21(3):217–28. doi: 10.1002/humu.10179 12619107.

13. Wang NJ, Sanborn Z, Arnett KL, Bayston LJ, Liao W, Proby CM, et al. Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Proc Natl Acad Sci U S A. 2011;108(43):17761–6. doi: 10.1073/pnas.1114669108 22006338; PubMed Central PMCID: PMC3203814.

14. Cammareri P, Rose AM, Vincent DF, Wang J, Nagano A, Libertini S, et al. Inactivation of TGFbeta receptors in stem cells drives cutaneous squamous cell carcinoma. Nat Commun. 2016;7:12493. doi: 10.1038/ncomms12493 27558455; PubMed Central PMCID: PMC5007296.

15. Lambert SR, Mladkova N, Gulati A, Hamoudi R, Purdie K, Cerio R, et al. Key differences identified between actinic keratosis and cutaneous squamous cell carcinoma by transcriptome profiling. Br J Cancer. 2014;110(2):520–9. doi: 10.1038/bjc.2013.760 24335922; PubMed Central PMCID: PMC3899778.

16. Masferrer E, Ferrandiz-Pulido C, Lloveras B, Masferrer-Niubo M, Espinet B, Salido M, et al. MYC copy number gains are associated with poor outcome in penile squamous cell carcinoma. J Urol. 2012;188(5):1965–71. doi: 10.1016/j.juro.2012.07.003 22999547.

17. Su F, Viros A, Milagre C, Trunzer K, Bollag G, Spleiss O, et al. RAS mutations in cutaneous squamous-cell carcinomas in patients treated with BRAF inhibitors. N Engl J Med. 2012;366(3):207–15. doi: 10.1056/NEJMoa1105358 22256804; PubMed Central PMCID: PMC3724537.

18. Toll A, Salgado R, Yebenes M, Martin-Ezquerra G, Gilaberte M, Baro T, et al. Epidermal growth factor receptor gene numerical aberrations are frequent events in actinic keratoses and invasive cutaneous squamous cell carcinomas. Exp Dermatol. 2010;19(2):151–3. doi: 10.1111/j.1600-0625.2009.01028.x 20156290.

19. Yadav V, Denning MF. Fyn is induced by Ras/PI3K/Akt signaling and is required for enhanced invasion/migration. Mol Carcinog. 2011;50(5):346–52. doi: 10.1002/mc.20716 21480388; PubMed Central PMCID: PMC3080437.

20. Sekulic A, Kim SY, Hostetter G, Savage S, Einspahr JG, Prasad A, et al. Loss of inositol polyphosphate 5-phosphatase is an early event in development of cutaneous squamous cell carcinoma. Cancer Prev Res (Phila). 2010;3(10):1277–83. doi: 10.1158/1940-6207.CAPR-10-0058 20876729; PubMed Central PMCID: PMC2955780.

21. Yadav V, Yanez NC, Fenton SE, Denning MF. Loss of protein kinase C delta gene expression in human squamous cell carcinomas: a laser capture microdissection study. Am J Pathol. 2010;176(3):1091–6. doi: 10.2353/ajpath.2010.090816 20093486; PubMed Central PMCID: PMC2832131.

22. Brown VL, Harwood CA, Crook T, Cronin JG, Kelsell DP, Proby CM. p16INK4a and p14ARF tumor suppressor genes are commonly inactivated in cutaneous squamous cell carcinoma. J Invest Dermatol. 2004;122(5):1284–92. doi: 10.1111/j.0022-202X.2004.22501.x 15140233.

23. Rodriguez-Paredes M, Esteller M. Cancer epigenetics reaches mainstream oncology. Nat Med. 2011;17(3):330–9. doi: 10.1038/nm.2305 21386836.

24. Ehrlich M, Lacey M. DNA hypomethylation and hemimethylation in cancer. Adv Exp Med Biol. 2013;754:31–56. doi: 10.1007/978-1-4419-9967-2_2 22956495.

25. Sandoval J, Esteller M. Cancer epigenomics: beyond genomics. Curr Opin Genet Dev. 2012;22(1):50–5. doi: 10.1016/j.gde.2012.02.008 22402447.

26. Chiles MC, Ai L, Zuo C, Fan CY, Smoller BR. E-cadherin promoter hypermethylation in preneoplastic and neoplastic skin lesions. Mod Pathol. 2003;16(10):1014–8. doi: 10.1097/01.MP.0000089779.35435.9D 14559984.

27. Murao K, Kubo Y, Ohtani N, Hara E, Arase S. Epigenetic abnormalities in cutaneous squamous cell carcinomas: frequent inactivation of the RB1/p16 and p53 pathways. Br J Dermatol. 2006;155(5):999–1005. doi: 10.1111/j.1365-2133.2006.07487.x 17034532.

28. Takeuchi T, Liang SB, Matsuyoshi N, Zhou S, Miyachi Y, Sonobe H, et al. Loss of T-cadherin (CDH13, H-cadherin) expression in cutaneous squamous cell carcinoma. Lab Invest. 2002;82(8):1023–9. doi: 10.1097/01.lab.0000025391.35798.f1 12177241.

29. Venza I, Visalli M, Tripodo B, De Grazia G, Loddo S, Teti D, et al. FOXE1 is a target for aberrant methylation in cutaneous squamous cell carcinoma. Br J Dermatol. 2010;162(5):1093–7. doi: 10.1111/j.1365-2133.2009.09560.x 19845668.

30. Liang J, Kang X, Halifu Y, Zeng X, Jin T, Zhang M, et al. Secreted frizzled-related protein promotors are hypermethylated in cutaneous squamous carcinoma compared with normal epidermis. BMC Cancer. 2015;15:641. doi: 10.1186/s12885-015-1650-x 26394929; PubMed Central PMCID: PMC4579584.

31. Darr OA, Colacino JA, Tang AL, McHugh JB, Bellile EL, Bradford CR, et al. Epigenetic alterations in metastatic cutaneous carcinoma. Head Neck. 2015;37(7):994–1001. doi: 10.1002/hed.23701 24700717; PubMed Central PMCID: PMC4183742.

32. Meier K, Drexler SK, Eberle FC, Lefort K, Yazdi AS. Silencing of ASC in Cutaneous Squamous Cell Carcinoma. PLoS One. 2016;11(10):e0164742. doi: 10.1371/journal.pone.0164742 27768771; PubMed Central PMCID: PMC5074456.

33. Nobeyama Y, Watanabe Y, Nakagawa H. Silencing of G0/G1 switch gene 2 in cutaneous squamous cell carcinoma. PLoS One. 2017;12(10):e0187047. doi: 10.1371/journal.pone.0187047 29073263; PubMed Central PMCID: PMC5658152.

34. Li L, Jiang M, Feng Q, Kiviat NB, Stern JE, Hawes S, et al. Aberrant Methylation Changes Detected in Cutaneous Squamous Cell Carcinoma of Immunocompetent Individuals. Cell Biochem Biophys. 2015;72(2):599–604. doi: 10.1007/s12013-014-0507-2 25575897.

35. Toll A, Salgado R, Espinet B, Diaz-Lagares A, Hernandez-Ruiz E, Andrades E, et al. MiR-204 silencing in intraepithelial to invasive cutaneous squamous cell carcinoma progression. Mol Cancer. 2016;15(1):53. doi: 10.1186/s12943-016-0537-z 27457246; PubMed Central PMCID: PMC4960761.

36. Venza M, Visalli M, Catalano T, Beninati C, Teti D, Venza I. DSS1 promoter hypomethylation and overexpression predict poor prognosis in melanoma and squamous cell carcinoma patients. Hum Pathol. 2017;60:137–46. doi: 10.1016/j.humpath.2016.10.018 27825810.

37. Ahuja N, Sharma AR, Baylin SB. Epigenetic Therapeutics: A New Weapon in the War Against Cancer. Annu Rev Med. 2016;67:73–89. doi: 10.1146/annurev-med-111314-035900 26768237; PubMed Central PMCID: PMC4937439.

38. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, et al. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013;10(10):949–55. doi: 10.1038/nmeth.2632 24076989.

39. Vandiver AR, Irizarry RA, Hansen KD, Garza LA, Runarsson A, Li X, et al. Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biol. 2015;16:80. doi: 10.1186/s13059-015-0644-y 25886480; PubMed Central PMCID: PMC4423110.

40. Rodriguez-Paredes M, Bormann F, Raddatz G, Gutekunst J, Lucena-Porcel C, Kohler F, et al. Methylation profiling identifies two subclasses of squamous cell carcinoma related to distinct cells of origin. Nat Commun. 2018;9(1):577. doi: 10.1038/s41467-018-03025-1 29422656; PubMed Central PMCID: PMC5805678.

41. Amin MB, Edge S, Greene F, Byrd DR, Brookland RK, Washington MK, et al. AJCC Cancer Staging Manual. 8 ed. New York: Springer International Publishing; 2007.

42. Moran S, Arribas C, Esteller M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics. 2016;8(3):389–99. doi: 10.2217/epi.15.114 26673039; PubMed Central PMCID: PMC4864062.

43. Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics. 2011;6(6):692–702. doi: 10.4161/epi.6.6.16196 21593595.

44. Sandoval J, Mendez-Gonzalez J, Nadal E, Chen G, Carmona FJ, Sayols S, et al. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. J Clin Oncol. 2013;31(32):4140–7. doi: 10.1200/JCO.2012.48.5516 24081945.

45. Zou H, Hastie T. Regularization and variable selection via the elastic net. Journal of the Royal Statistical Society: Series B (Statistical Methodology). 2005;67(2):301–20. doi: 10.1111/j.1467-9868.2005.00503.x

46. Ferrari S, Cribari-Neto F. Beta Regression for Modelling Rates and Proportions. Journal of Applied Statistics. 2004;31(7):799–815. doi: 10.1080/0266476042000214501

47. Ge S, Jung D. ShinyGO: a graphical enrichment tool for animals and plants. bioRxiv. 2018:315150. doi: 10.1101/315150

48. Bangdiwala SI, Haedo AS, Natal ML, Villaveces A. The agreement chart as an alternative to the receiver-operating characteristic curve for diagnostic tests. J Clin Epidemiol. 2008;61(9):866–74. doi: 10.1016/j.jclinepi.2008.04.002 18687288.

49. Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M. New approach for understanding genome variations in KEGG. Nucleic Acids Res. 2019;47(D1):D590–D5. doi: 10.1093/nar/gky962 30321428; PubMed Central PMCID: PMC6324070.

50. van Doorn R, Gruis NA, Willemze R, van der Velden PA, Tensen CP. Aberrant DNA methylation in cutaneous malignancies. Semin Oncol. 2005;32(5):479–87. doi: 10.1053/j.seminoncol.2005.07.001 16210089.

51. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009;41(2):178–86. doi: 10.1038/ng.298 19151715; PubMed Central PMCID: PMC2729128.

52. Inoue K, Fry EA. Alterations of p63 and p73 in Human Cancers. In: Deb SP, Deb S, editors. Mutant p53 and MDM2 in Cancer. Dordrecht: Springer Netherlands; 2014. p. 17–40.

53. Pflaum J, Schlosser S, Muller M. p53 Family and Cellular Stress Responses in Cancer. Front Oncol. 2014;4:285. doi: 10.3389/fonc.2014.00285 25374842; PubMed Central PMCID: PMC4204435.

54. Rodriguez N, Pelaez A, Barderas R, Dominguez G. Clinical implications of the deregulated TP73 isoforms expression in cancer. Clin Transl Oncol. 2018;20(7):827–36. doi: 10.1007/s12094-017-1802-3 29230693.

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2019 Číslo 12
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