Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet. 2012;13:679–92. https://doi.org/10.1038/nrg3270.
Article
CAS
PubMed
Google Scholar
Fong PC, Yap TA, Boss DS, Carden CP, Mergui-Roelvink M, Gourley C, De Greve J, Lubinski J, Shanley S, Messiou C, A’Hern R, Tutt A, Ashworth A, Stone J, Carmichael J, Schellens JH, de Bono JS, Kaye SB. Poly(ADP)-ribose polymerase inhibition: frequent durable responses in BRCA carrier ovarian cancer correlating with platinum-free interval. J Clin Oncol. 2010;28:2512–9. https://doi.org/10.1200/JCO.2009.26.9589.
Article
CAS
PubMed
Google Scholar
Dejeux E, Ronneberg JA, Solvang H, Bukholm I, Geisler S, Aas T, Gut IG, Borresen-Dale AL, Lonning PE, Kristensen VN, Tost J. DNA methylation profiling in doxorubicin treated primary locally advanced breast tumours identifies novel genes associated with survival and treatment response. Mol Cancer. 2010;9:68. https://doi.org/10.1186/1476-4598-9-68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chekhun VF, Kulik GI, Yurchenko OV, Tryndyak VP, Todor IN, Luniv LS, Tregubova NA, Pryzimirska TV, Montgomery B, Rusetskaya NV, Pogribny IP. Role of DNA hypomethylation in the development of the resistance to doxorubicin in human MCF-7 breast adenocarcinoma cells. Cancer Lett. 2006;231:87–93. https://doi.org/10.1016/j.canlet.2005.01.038.
Article
CAS
PubMed
Google Scholar
Ai L, Kim WJ, Demircan B, Dyer LM, Bray KJ, Skehan RR, Massoll NA, Brown KD. The transglutaminase 2 gene (TGM2), a potential molecular marker for chemotherapeutic drug sensitivity, is epigenetically silenced in breast cancer. Carcinogenesis. 2008;29:510–8. https://doi.org/10.1093/carcin/bgm280.
Article
CAS
PubMed
Google Scholar
Balko JM, Cook RS, Vaught DB, Kuba MG, Miller TW, Bhola NE, Sanders ME, Granja-Ingram NM, Smith JJ, Meszoely IM, Salter J, Dowsett M, Stemke-Hale K, González-Angulo AM, Mills GB, Pinto JA, Gómez HL, Arteaga CL. Profiling of residual breast cancers after neoadjuvant chemotherapy identifies DUSP4 deficiency as a mechanism of drug resistance. Nat Med. 2012;18:1052–9. https://doi.org/10.1038/nm.2795.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maier S, Nimmrich I, Koenig T, Eppenberger-Castori S, Bohlmann I, Paradiso A, Spyratos F, Thomssen C, Mueller V, Nahrig J, Schittulli F, Kates R, Lesche R, Schwope I, Kluth A, Marx A, Martens JW, Foekens JA, Schmitt M, Harbeck N, European Organisation for Research and Treatment of Cancer (EORTC) PathoBiology group. DNA-methylation of the homeodomain transcription factor PITX2 reliably predicts risk of distant disease recurrence in tamoxifen-treated, node-negative breast cancer patients–Technical and clinical validation in a multi-centre setting in collaboration with the European Organisation for Research and Treatment of Cancer (EORTC) PathoBiology group. Eur J Cancer. 2007;43:1679–86. https://doi.org/10.1016/j.ejca.2007.04.025.
Article
CAS
PubMed
Google Scholar
Iorns E, Turner NC, Elliott R, Syed N, Garrone O, Gasco M, Tutt AN, Crook T, Lord CJ, Ashworth A. Identification of CDK10 as an important determinant of resistance to endocrine therapy for breast cancer. Cancer Cell. 2008;13:91–104. https://doi.org/10.1016/j.ccr.2008.01.001.
Article
CAS
PubMed
Google Scholar
Brocks D, Assenov Y, Minner S, Bogatyrova O, Simon R, Koop C, Oakes C, Zucknick M, Lipka DB, Weischenfeldt J, Feuerbach L, Cowper-Sal Lari R, Lupien M, Brors B, Korbel J, Schlomm T, Tanay A, Sauter G, Gerhäuser C, Plass C, ICGC Early Onset Prostate Cancer Project. Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer. Cell Rep. 2014;8:798–806. https://doi.org/10.1016/j.celrep.2014.06.053.
Article
CAS
PubMed
Google Scholar
Luo Y, Li J, Zhu D, Fan Y, Li S, Sun X. High-resolution chromosomal microarray analysis of early-stage human embryonic stem cells reveals an association between X chromosome instability and skewed X inactivation. Cell Biosci 2014;4(1):74.
Article
PubMed
PubMed Central
Google Scholar
Jeschke J, Bizet M, Desmedt C, Calonne E, Dedeurwaerder S, Garaud S, Koch A, Larsimont D, Salgado R, Van den Eynden G, Willard Gallo K, Bontempi G, Defrance M, Sotiriou C, Fuks F. DNA methylation-based immune response signature improves patient diagnosis in multiple cancers. J Clin Invest. 2017;127:3090–102. https://doi.org/10.1172/JCI91095.
Article
PubMed
PubMed Central
Google Scholar
Sandhu R, Roll JD, Rivenbark AG, Coleman WB. Dysregulation of the epigenome in human breast cancer: contributions of gene-specific DNA hypermethylation to breast cancer pathobiology and targeting the breast cancer methylome for improved therapy. Am J Pathol. 2015;185:282–92. https://doi.org/10.1016/j.ajpath.2014.12.003.
Article
CAS
PubMed
Google Scholar
Witte T, Plass C, Gerhauser C. Pan-cancer patterns of DNA methylation. Genome Med. 2014;6:66. https://doi.org/10.1186/s13073-014-0066-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moelans CB, de Groot JS, Pan X, van der Wall E, van Diest PJ. Clonal intratumor heterogeneity of promoter hypermethylation in breast cancer by MS-MLPA. Mod Pathol. 2014;27:869–74. https://doi.org/10.1038/modpathol.2013.207.
Article
CAS
PubMed
Google Scholar
Pidsley R, Wong CC, Volta M, Lunnon K, Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics. 2013;14:293. https://doi.org/10.1186/1471-2164-14-293.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morris TJ, Butcher LM, Feber A, Teschendorff AE, Chakravarthy AR, Wojdacz TK, Beck S. ChAMP: 450k chip analysis methylation pipeline. Bioinformatics. 2014;30:428–30. https://doi.org/10.1093/bioinformatics/btt684.
Article
CAS
PubMed
Google Scholar
Peters TJ, Buckley MJ, Statham AL, Pidsley R, Samaras K, Lord RV, Clark SJ, Molloy PL. De novo identification of differentially methylated regions in the human genome. Epigenet Chromatin. 2015;8:6. https://doi.org/10.1186/1756-8935-8-6.
Article
CAS
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57. https://doi.org/10.1038/nprot.2008.211.
Article
CAS
Google Scholar
Weisenberger DJ, Trinh BN, Campan M, Sharma S, Long TI, Ananthnarayan S, Liang G, Esteva FJ, Hortobagyi GN, McCormick F, Jones PA, Laird PW. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res. 2015;36:4689–98. https://doi.org/10.1093/nar/gkn455.
Article
CAS
Google Scholar
Szyf M. DNA methylation signatures for breast cancer classification and prognosis. Genome Med. 2012;4:26. https://doi.org/10.1186/gm325.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol. 2009;27:1160–7. https://doi.org/10.1200/JCO.2008.18.1370.
Article
PubMed
PubMed Central
Google Scholar
He DX, Gu XT, Jiang L, Jin J, Ma X. A methylation-based regulatory network for microRNA 320a in chemoresistant breast cancer. Mol Pharmacol. 2014;86:536–47. https://doi.org/10.1124/mol.114.092759.
Article
CAS
PubMed
Google Scholar
Foo LC, Dougherty JD. Aldh1L1 is expressed by postnatal neural stem cells in vivo. Glia. 2013;61:1533–41. https://doi.org/10.1002/glia.22539.
Article
PubMed
PubMed Central
Google Scholar
Mariotto A, Pavlova O, Park HS, Huber M, Hohl D. HOPX: the unusual homeodomain-containing protein. J Invest Dermatol. 2016;136:905–11. https://doi.org/10.1016/j.jid.2016.01.032.
Article
CAS
PubMed
Google Scholar
Nemeth MJ, Topol L, Anderson SM, Yang Y, Bodine DM. Wnt5a inhibits canonical Wnt signaling in hematopoietic stem cells and enhances repopulation. Proc Natl Acad Sci USA. 2007;104:15436–41. https://doi.org/10.1073/pnas.0704747104.
Article
PubMed
PubMed Central
Google Scholar
Chavali M, Klingener M, Kokkosis AG, Garkun Y, Felong S, Maffei A, Aguirre A. Non-canonical Wnt signaling regulates neural stem cell quiescence during homeostasis and after demyelination. Nat Commun. 2018;9:36. https://doi.org/10.1038/s41467-017-02440-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
Richmond CA, Shah MS, Carlone DL, Breault DT. Factors regulating quiescent stem cells: insights from the intestine and other self-renewing tissues. J Physiol. 2016;594:4805–13. https://doi.org/10.1113/JP271653.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dickinson RE, Dallol A, Bieche I, Krex D, Morton D, Maher ER, Latif F. Epigenetic inactivation of SLIT3 and SLIT1 genes in human cancers. Br J Cancer. 2004;91:2071–8. https://doi.org/10.1038/sj.bjc.6602222.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berman H, Zhang J, Crawford YG, Gauthier ML, Fordyce CA, McDermott KM, Sigaroudinia M, Kozakiewicz K, Tlsty TD. Genetic and epigenetic changes in mammary epithelial cells identify a subpopulation of cells involved in early carcinogenesis. Cold Spring Harb Symp Quant Biol. 2005;70:317–27. https://doi.org/10.1101/sqb.2005.70.051.
Article
CAS
PubMed
Google Scholar
Pan H, Jiang Y, Boi M, Tabbo F, Redmond D, Nie K, Ladetto M, Chiappella A, Cerchietti L, Shaknovich R, Melnick AM, Inghirami GG, Tam W, Elemento O. Epigenomic evolution in diffuse large B-cell lymphomas. Nat Commun. 2015;6:6921. https://doi.org/10.1038/ncomms7921.
Article
CAS
PubMed
Google Scholar
Insel PA, Zhang L, Murray F, Yokouchi H, Zambon AC. Cyclic AMP is both a pro-apoptotic and anti-apoptotic second messenger. Acta Physiol (Oxf). 2012;204:277–87. https://doi.org/10.1111/j.1748-1716.2011.02273.x.
Article
CAS
Google Scholar
Lin H, Lin Q, Liu M, Lin Y, Wang X, Chen H, Xia Z, Lu B, Ding F, Wu Q, Wang HR. PKA/Smurf1 signaling-mediated stabilization of Nur77 is required for anticancer drug cisplatin-induced apoptosis. Oncogene. 2014;33:1629–39. https://doi.org/10.1038/onc.2013.116.
Article
CAS
PubMed
Google Scholar
Rukoyatkina N, Butt E, Subramanian H, Nikolaev VO, Mindukshev I, Walter U, Gambaryan S, Benz PM. Protein kinase A activation by the anti-cancer drugs ABT-737 and thymoquinone is caspase-3-dependent and correlates with platelet inhibition and apoptosis. Cell Death Dis. 2017;8:e2898. https://doi.org/10.1038/cddis.2017.290.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dimitrova N, Nagaraj AB, Razi A, Singh S, Kamalakaran S, Banerjee N, Joseph P, Mankovich A, Mittal P, DiFeo A, Varadan V. InFlo: a novel systems biology framework identifies cAMP-CREB1 axis as a key modulator of platinum resistance in ovarian cancer. Oncogene. 2017;36:2472–82. https://doi.org/10.1038/onc.2016.398.
Article
CAS
PubMed
Google Scholar
Yu T, Yang G, Hou Y, Tang X, Wu C, Wu XA, Guo L, Zhu Q, Luo H, Du YE, Wen S, Xu L, Yin J, Tu G, Liu M. Cytoplasmic GPER translocation in cancer-associated fibroblasts mediates cAMP/PKA/CREB/glycolytic axis to confer tumor cells with multidrug resistance. Oncogene. 2017;36:2131–45. https://doi.org/10.1038/onc.2016.370.
Article
CAS
PubMed
Google Scholar
Ducker GS, Rabinowitz JD. One-carbon metabolism in health and disease. Cell Metab. 2017;25:27–42. https://doi.org/10.1016/j.cmet.2016.08.009.
Article
CAS
PubMed
Google Scholar
Zhu D, Zhao Z, Cui G, Chang S, Hu L, See YX, Lim MGL, Guo D, Chen X, Robson P, Luo Y, Cheung E. Single-cell transcriptome analysis reveals estrogen signaling coordinately augments one-carbon, polyamine, and purine synthesis in breast cancer. Cell Rep. 2018;25:2285–98. https://doi.org/10.1016/j.celrep.2018.10.093.
Article
CAS
PubMed
Google Scholar
Sosa MS, Parikh F, Maia AG, Estrada Y, Bosch A, Bragado P, Ekpin E, George A, Zheng Y, Lam HM, Morrissey C, Chung CY, Farias EF, Bernstein E, Aguirre-Ghiso JA. NR2F1 controls tumour cell dormancy via SOX9- and RARβ-driven quiescence programmes. Nat Commun. 2015;6:6170. https://doi.org/10.1038/ncomms7170.
Article
CAS
PubMed
Google Scholar
Luo Y, Xu X, An X, Sun X, Wang S, Zhu D. Targeted inhibition of the miR-199a/214 cluster by CRISPR interference augments the tumor tropism of human induced pluripotent stem cell-derived neural stem cells under hypoxic condition. Stem Cells Int 2016;2016:1–8.
Article
Google Scholar
Luo Y, Zhu D, Zhang Z, Chen Y, Sun X. Integrative analysis of CRISPR/Cas9 target sites in the human gene. BioMed Res Int 2015;2015:1–9.
Google Scholar
Luo Y, Zhu D, Lam DH, Huang J, Tang Y, Luo X, Wang S. A double-switch cell fusion-inducible transgene expression system for neural stem cell-based antiglioma gene therapy. Stem Cells Int 2015;2015:1–8.
Article
Google Scholar
Luo Y, Zhu D. Combinatorial control of transgene expression by hypoxia-responsive promoter and microRNA regulation for neural stem cell-based cancer therapy. BioMed Res Int 2014;2014:1–9.
Google Scholar