Top

Published in:

01-02-2015 | Epidemiology

Methylation profiling of 48 candidate genes in tumor and matched normal tissues from breast cancer patients

Authors: Zibo Li, Xinwu Guo, Yepeng Wu, Shengyun Li, Jinhua Yan, Limin Peng, Zhi Xiao, Shouman Wang, Zhongping Deng, Lizhong Dai, Wenjun Yi, Kun Xia, Lili Tang, Jun Wang

Published in: Breast Cancer Research and Treatment | Issue 3/2015

Abstract

Gene-specific methylation alterations in breast cancer have been suggested to occur early in tumorigenesis and have the potential to be used for early detection and prevention. The continuous increase in worldwide breast cancer incidences emphasizes the urgent need for identification of methylation biomarkers for early cancer detection and patient stratification. Using microfluidic PCR-based target enrichment and next-generation bisulfite sequencing technology, we analyzed methylation status of 48 candidate genes in paired tumor and normal tissues from 180 Chinese breast cancer patients. Analysis of the sequencing results showed 37 genes differentially methylated between tumor and matched normal tissues. Breast cancer samples with different clinicopathologic characteristics demonstrated distinct profiles of gene methylation. The methylation levels were significantly different between breast cancer subtypes, with basal-like and luminal B tumors having the lowest and the highest methylation levels, respectively. Six genes (ACADL, ADAMTSL1, CAV1, NPY, PTGS2, and RUNX3) showed significant differential methylation among the 4 breast cancer subtypes and also between the ER +/ER- tumors. Using unsupervised hierarchical clustering analysis, we identified a panel of 13 hypermethylated genes as candidate biomarkers that performed a high level of efficiency for cancer prediction. These 13 genes included CST6, DBC1, EGFR, GREM1, GSTP1, IGFBP3, PDGFRB, PPM1E, SFRP1, SFRP2, SOX17, TNFRSF10D, and WRN. Our results provide evidence that well-defined DNA methylation profiles enable breast cancer prediction and patient stratification. The novel gene panel might be a valuable biomarker for early detection of breast cancer.

Available only for authorised users

Ferlay J SI, Ervik M, Dikshit R, Eser S, Mathers C, Rebelo M, Parkin DM, Forman D, Bray F (2013) GLOBOCAN 2012 v1.0, cancer incidence and mortality worldwide: IARC CancerBase No. 11 [Internet]. International Agency for Research on Cancer, Lyon. http://globocan.iarc.fr. Accessed on 17 Aug 2014

Etzioni R, Urban N, Ramsey S, McIntosh M, Schwartz S, Reid B, Radich J, Anderson G, Hartwell L (2003) The case for early detection. Nat Rev Cancer 3(4):243–252. doi:10.1038/nrc1041 CrossRefPubMed

Feinberg AP, Ohlsson R, Henikoff S (2006) The epigenetic progenitor origin of human cancer. Nat Rev Genet 7(1):21–33. doi:10.1038/nrg1748 CrossRefPubMed

Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128(4):683–692. doi:10.1016/j.cell.2007.01.029 CrossRefPubMedCentralPubMed

Suijkerbuijk KP, van Diest PJ, van der Wall E (2011) Improving early breast cancer detection: focus on methylation. Ann Oncol 22(1):24–29. doi:10.1093/annonc/mdq305 CrossRefPubMed

Esteller M (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8(4):286–298. doi:10.1038/nrg2005 CrossRefPubMed

Radpour R, Barekati Z, Kohler C, Lv Q, Burki N, Diesch C, Bitzer J, Zheng H, Schmid S, Zhong XY (2011) Hypermethylation of tumor suppressor genes involved in critical regulatory pathways for developing a blood-based test in breast cancer. PLoS One 6(1):e16080. doi:10.1371/journal.pone.0016080 CrossRefPubMedCentralPubMed

Fackler MJ, Bujanda ZL, Umbricht C, Teo WW, Cho S, Zhang Z, Visvanathan K, Jeter S, Argani P, Wang C, Lyman JP, de Brot M, Ingle JN, Boughey J, McGuire K, King TA, Carey LA, Cope L, Wolff AC, Sukumar S (2014) Novel methylated biomarkers and a robust assay to detect circulating tumor DNA in metastatic breast cancer. Cancer Res 74(8):2160–2170. doi:10.1158/0008-5472.CAN-13-3392 CrossRefPubMed

Chan KC, Jiang P, Chan CW, Sun K, Wong J, Hui EP, Chan SL, Chan WC, Hui DS, Ng SS, Chan HL, Wong CS, Ma BB, Chan AT, Lai PB, Sun H, Chiu RW, Lo YM (2013) Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci USA 110(47):18761–18768. doi:10.1073/pnas.1313995110 CrossRefPubMedCentralPubMed

10.

Kloten V, Becker B, Winner K, Schrauder MG, Fasching PA, Anzeneder T, Veeck J, Hartmann A, Knuchel R, Dahl E (2013) Promoter hypermethylation of the tumor-suppressor genes ITIH5, DKK3, and RASSF1A as novel biomarkers for blood-based breast cancer screening. Breast Cancer Res 15(1):R4. doi:10.1186/bcr3375 CrossRefPubMedCentralPubMed

11.

Feng W, Shen L, Wen S, Rosen DG, Jelinek J, Hu X, Huan S, Huang M, Liu J, Sahin AA, Hunt KK, Bast RC Jr, Shen Y, Issa JP, Yu Y (2007) Correlation between CpG methylation profiles and hormone receptor status in breast cancers. Breast Cancer Res 9(4):R57. doi:10.1186/bcr1762 CrossRefPubMedCentralPubMed

12.

Fiegl H, Millinger S, Goebel G, Muller-Holzner E, Marth C, Laird PW, Widschwendter M (2006) Breast cancer DNA methylation profiles in cancer cells and tumor stroma: association with HER-2/neu status in primary breast cancer. Cancer Res 66(1):29–33. doi:10.1158/0008-5472.CAN-05-2508 CrossRefPubMed

13.

Bediaga NG, Acha-Sagredo A, Guerra I, Viguri A, Albaina C, Ruiz Diaz I, Rezola R, Alberdi MJ, Dopazo J, Montaner D, Renobales M, Fernandez AF, Field JK, Fraga MF, Liloglou T, de Pancorbo MM (2010) DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res 12(5):R77. doi:10.1186/bcr2721 CrossRefPubMedCentralPubMed

14.

Holm K, Hegardt C, Staaf J, Vallon-Christersson J, Jonsson G, Olsson H, Borg A, Ringner M (2010) Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res 12(3):R36. doi:10.1186/bcr2590 CrossRefPubMedCentralPubMed

15.

Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G (2010) Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics 11:137. doi:10.1186/1471-2164-11-137 CrossRefPubMedCentralPubMed

16.

Hill VK, Ricketts C, Bieche I, Vacher S, Gentle D, Lewis C, Maher ER, Latif F (2011) Genome-wide DNA methylation profiling of CpG islands in breast cancer identifies novel genes associated with tumorigenicity. Cancer Res 71(8):2988–2999. doi:10.1158/0008-5472.CAN-10-4026 CrossRefPubMed

17.

Fackler MJ, Umbricht CB, Williams D, Argani P, Cruz LA, Merino VF, Teo WW, Zhang Z, Huang P, Visvananthan K, Marks J, Ethier S, Gray JW, Wolff AC, Cope LM, Sukumar S (2011) Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence. Cancer Res 71(19):6195–6207. doi:10.1158/0008-5472.CAN-11-1630 CrossRefPubMedCentralPubMed

18.

Cancer Genome Atlas N (2012) Comprehensive molecular portraits of human breast tumours. Nature 490(7418):61–70. doi:10.1038/nature11412 CrossRef

19.

Cornen S, Guille A, Adelaide J, Addou-Klouche L, Finetti P, Saade MR, Manai M, Carbuccia N, Bekhouche I, Letessier A, Raynaud S, Charafe-Jauffret E, Jacquemier J, Spicuglia S, de The H, Viens P, Bertucci F, Birnbaum D, Chaffanet M (2014) Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling. PLoS One 9(1):e81843. doi:10.1371/journal.pone.0081843 CrossRefPubMedCentralPubMed

20.

Goldhirsch A, Winer EP, Coates AS, Gelber RD, Piccart-Gebhart M, Thurlimann B, Senn HJ, Panel members (2013) Personalizing the treatment of women with early breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2013. Ann Oncol 24(9):2206–2223. doi:10.1093/annonc/mdt303 CrossRefPubMedCentralPubMed

21.

Varley KE, Mitra RD (2010) Bisulfite patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res 20(9):1279–1287. doi:10.1101/gr.101212.109 CrossRefPubMedCentralPubMed

22.

Flanagan JM, Cocciardi S, Waddell N, Johnstone CN, Marsh A, Henderson S, Simpson P, da Silva L, kConFab Investigators, Khanna K, Lakhani S, Boshoff C, Chenevix-Trench G (2010) DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status. Am J Hum Genet 86(3):420–433. doi:10.1016/j.ajhg.2010.02.008 CrossRefPubMedCentralPubMed

23.

Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6(2):65–70

24.

Hollants S, Redeker EJ, Matthijs G (2012) Microfluidic amplification as a tool for massive parallel sequencing of the familial hypercholesterolemia genes. Clin Chem 58(4):717–724. doi:10.1373/clinchem.2011.173963 CrossRefPubMed

25.

Bourgon R, Lu S, Yan Y, Lackner MR, Wang W, Weigman V, Wang D, Guan Y, Ryner L, Koeppen H, Patel R, Hampton GM, Amler LC, Wang Y (2014) High-throughput detection of clinically relevant mutations in archived tumor samples by multiplexed PCR and next-generation sequencing. Clin Cancer Res 20(8):2080–2091. doi:10.1158/1078-0432.CCR-13-3114 CrossRefPubMed

26.

Klajic J, Fleischer T, Dejeux E, Edvardsen H, Warnberg F, Bukholm I, Lonning PE, Solvang H, Borresen-Dale AL, Tost J, Kristensen VN (2013) Quantitative DNA methylation analyses reveal stage dependent DNA methylation and association to clinico-pathological factors in breast tumors. BMC Cancer 13:456. doi:10.1186/1471-2407-13-456 CrossRefPubMedCentralPubMed

27.

Heyn H, Moran S, Hernando-Herraez I, Sayols S, Gomez A, Sandoval J, Monk D, Hata K, Marques-Bonet T, Wang L, Esteller M (2013) DNA methylation contributes to natural human variation. Genome Res 23(9):1363–1372. doi:10.1101/gr.154187.112 CrossRefPubMedCentralPubMed

28.

Xia YY, Ding YB, Liu XQ, Chen XM, Cheng SQ, Li LB, Ma MF, He JL (1846) Wang YX (2014) Racial/ethnic disparities in human DNA methylation. Biochim Biophys Acta 1:258–262. doi:10.1016/j.bbcan.2014.07.001

29.

Ambrosone CB, Young AC, Sucheston LE, Wang D, Yan L, Liu S, Tang L, Hu Q, Freudenheim JL, Shields PG, Morrison CD, Demissie K, Higgins MJ (2014) Genome-wide methylation patterns provide insight into differences in breast tumor biology between American women of African and European ancestry. Oncotarget 5(1):237–248PubMedCentralPubMed

30.

Radpour R, Kohler C, Haghighi MM, Fan AX, Holzgreve W, Zhong XY (2009) Methylation profiles of 22 candidate genes in breast cancer using high-throughput MALDI-TOF mass array. Oncogene 28(33):2969–2978. doi:10.1038/onc.2009.149 CrossRefPubMed

31.

Hartmann O, Spyratos F, Harbeck N, Dietrich D, Fassbender A, Schmitt M, Eppenberger-Castori S, Vuaroqueaux V, Lerebours F, Welzel K, Maier S, Plum A, Niemann S, Foekens JA, Lesche R, Martens JW (2009) DNA methylation markers predict outcome in node-positive, estrogen receptor-positive breast cancer with adjuvant anthracycline-based chemotherapy. Clin Cancer Res 15(1):315–323. doi:10.1158/1078-0432.CCR-08-0166 CrossRefPubMed

32.

Wojdacz TK, Windelov JA, Thestrup BB, Damsgaard TE, Overgaard J, Hansen L (2014) Identification and characterization of locus-specific methylation patterns within novel loci undergoing hypermethylation during breast cancer pathogenesis. Breast Cancer Res 16(1):R17. doi:10.1186/bcr3612 CrossRefPubMedCentralPubMed

33.

Twelves D, Nerurkar A, Osin P, Dexter T, Ward A, Gui GP, Isacke CM (2013) DNA promoter hypermethylation profiles in breast duct fluid. Breast Cancer Res Treat 139(2):341–350. doi:10.1007/s10549-013-2544-8 CrossRefPubMed

34.

Bardowell SA, Parker J, Fan C, Crandell J, Perou CM, Swift-Scanlan T (2013) Differential methylation relative to breast cancer subtype and matched normal tissue reveals distinct patterns. Breast Cancer Res Treat 142(2):365–380. doi:10.1007/s10549-013-2738-0 CrossRefPubMedCentralPubMed

35.

Lim E, Vaillant F, Wu D, Forrest NC, Pal B, Hart AH, Asselin-Labat ML, Gyorki DE, Ward T, Partanen A, Feleppa F, Huschtscha LI, Thorne HJ, kConFab, Fox SB, Yan M, French JD, Brown MA, Smyth GK, Visvader JE, Lindeman GJ (2009) Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nature Med 15(8):907–913. doi:10.1038/nm.2000 CrossRefPubMed

36.

Li L, Lee KM, Han W, Choi JY, Lee JY, Kang GH, Park SK, Noh DY, Yoo KY, Kang D (2010) Estrogen and progesterone receptor status affect genome-wide DNA methylation profile in breast cancer. Hum Mol Genet 19(21):4273–4277. doi:10.1093/hmg/ddq351 CrossRefPubMed

Title: Methylation profiling of 48 candidate genes in tumor and matched normal tissues from breast cancer patients
Authors: Zibo Li
Xinwu Guo
Yepeng Wu
Shengyun Li
Jinhua Yan
Limin Peng
Zhi Xiao
Shouman Wang
Zhongping Deng
Lizhong Dai
Wenjun Yi
Kun Xia
Lili Tang
Jun Wang
Publication date: 01-02-2015
Publisher: Springer US
Published in: Breast Cancer Research and Treatment / Issue 3/2015
Print ISSN: 0167-6806
Electronic ISSN: 1573-7217
DOI: https://doi.org/10.1007/s10549-015-3276-8

Webinar | 19-02-2024 | 17:30 (CET)

Keynote webinar | Spotlight on antibody–drug conjugates in cancer

Watch now

Antibody–drug conjugates (ADCs) are novel agents that have shown promise across multiple tumor types. Explore the current landscape of ADCs in breast and lung cancer with our experts, and gain insights into the mechanism of action, key clinical trials data, existing challenges, and future directions.

Dr. Véronique Diéras

Prof. Fabrice Barlesi

Developed by: Springer Medicine

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 3/2015

Genomic predictor of residual risk of recurrence after adjuvant chemotherapy and endocrine therapy in high risk estrogen receptor-positive breast cancers

Meta-analyses of etiologic studies should account for the underlying biologic mechanisms

Efficacy of physical examination, ultrasound, and ultrasound combined with fine-needle aspiration for axilla staging of primary breast cancer

DC-SCRIPT is a novel regulator of the tumor suppressor gene CDKN2B and induces cell cycle arrest in ERα-positive breast cancer cells

Effect of menstrual cycle and menopausal status on apparent diffusion coefficient values and detectability of invasive ductal carcinoma on diffusion-weighted MRI

Clinical outcomes in breast cancer patients with HIV/AIDS: a retrospective study

Keynote webinar | Spotlight on antibody–drug conjugates in cancer