Epigenetic stem cell signature in cancer

Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells

Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R., Chevalier, B. S., Johnstone, S. E., Cole, M. F., Isono, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.043 · Cited by 2,238 · see citing works

CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer

Weisenberger, D. J., Siegmund, K. D., Campan, M., Young, J. P., Long, T. I., Faasse, M. A., Kang, G. H., Widschwendter, M., Weener, D., Buchanan, D. D., et al. (2006) · Nature Genetics · doi:10.1038/ng1834 · Cited by 1,990 · see citing works

The epigenetic progenitor origin of human cancer

Feinberg, A. P., OHLSSON, R. I., & Henikoff, S. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1748 · Cited by 1,851 · see citing works

Cancer Stem Cells

Jordan, C. T., Guzmán, M. L., & Noble, M. (2006) · New England Journal of Medicine · doi:10.1056/nejmra061808 · Cited by 1,708 · see citing works

Applying the principles of stem-cell biology to cancer

Pardal, R., Clarke, M. F., & Morrison, S. J. (2003) · Nature reviews. Cancer · doi:10.1038/nrc1232 · Cited by 1,616 · see citing works

Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitionsPreprint

Bracken, A. P., Dietrich, N., Pasini, D., Hansen, K. H., & Helin, K. (2006) · Genes & Development · doi:10.1101/gad.381706 · Cited by 1,258 · see citing works

Epigenetic Regulation of Cellular Memory by the Polycomb and Trithorax Group Proteins

Ringrose, L., & Paro, R. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.38.072902.091907 · Cited by 1,077 · see citing works

Functional engraftment of human ES cell–derived dopaminergic neurons enriched by coculture with telomerase-immortalized midbrain astrocytes

Roy, N. S., Cléren, C., Singh, S. K., Yang, L., Beal, M. F., & Goldman, S. A. (2006) · Nature Medicine · doi:10.1038/nm1495 · Cited by 822 · see citing works

MGMT Promoter Methylation and Field Defect in Sporadic Colorectal Cancer

Shen, L., Kondo, Y., Rosner, G. L., Xiao, L., Hernandez, N., Vilaythong, J. N., Houlihan, P., Krouse, R. S., Prasad, A. R., Einspahr, J. G., et al. (2005) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/dji275 · Cited by 492 · see citing works

Fields of aberrant CpG island hypermethylation in Barrett's esophagus and associated adenocarcinoma.

Eads, C. A., Lord, R. V., Kurumboor, S. K., Wickramasinghe, K. S., Skinner, M. L., Long, T. I., Peters, J. H., DeMeester, T. R., Danenberg, K. D., Danenberg, P. V., et al. (2000) · PubMed · Cited by 366 · see citing works

Suz12 binds to silenced regions of the genome in a cell-type-specific mannerPreprint

Squazzo, S. L., O’Geen, H., Komashko, V., Krig, S. R., Jin, V. X., Jang, S.-W., Margueron, R., Reinberg, D., Green, R., & Farnham, P. (2006) · Genome Research · doi:10.1101/gr.5306606 · Cited by 310 · see citing works

Genome-wide profiling of promoter methylation in human

Hatada, I., Fukasawa, M., Kimura, M., Morita, S., Yamada, K., Yoshikawa, T., Yamanaka, S., Endo, C., Sakurada, A., Sato, M., et al. (2006) · Oncogene · doi:10.1038/sj.onc.1209331 · Cited by 147 · see citing works

Stem cells and cancer.

Houghton, J., Morozov, A., Smirnova, I., & Wang, T. C. (2007) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2006.04.003 · Cited by 58 · see citing works

CIMPle origin for promoter hypermethylation in colorectal cancer?

Schuebel, K. E., Chen, W., & Baylin, S. B. (2006) · Nature Genetics · doi:10.1038/ng0706-738 · Cited by 26 · see citing works

Cancer biology: A game of subversion

Passegué, E. (2006) · Nature · doi:10.1038/442754a · Cited by 13 · see citing works

Functions of DNA methylation: islands, start sites, gene bodies and beyond

Jones, P. A. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3230 · Cited by 6,061 · see citing works

CpG islands and the regulation of transcription

Deaton, A. M., & Bird, A. (2011) · Genes & Development · doi:10.1101/gad.2037511 · Cited by 3,187 · see citing works

A decade of exploring the cancer epigenome—biological and translational implications

Baylin, S. B., & Jones, P. A. (2011) · Nature Reviews Cancer · doi:10.1038/nrc3130 · Cited by 2,871 · see citing works

Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma

Ally, A., Balasundaram, M., Carlsen, R., Chuah, E., Clarke, A., Dhalla, N., Holt, R. A., Jones, S. J. M., Lee, D., Ma, Y., et al. (2017) · Cell · doi:10.1016/j.cell.2017.05.046 · Cited by 2,490 · see citing works

Epigenetics in cancer

Sharma, S., Kelly, T. K., & Jones, P. A. (2010) · Carcinogenesis · doi:10.1093/carcin/bgp220 · Cited by 2,637 · see citing works

Linking DNA methylation and histone modification: patterns and paradigms

Cedar, H., & Bergman, Y. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2540 · Cited by 2,267 · see citing works

Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer

Yang, X., Han, H., De Carvalho, D. D., Lay, F. D., Jones, P. A., & Liang, G. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.07.028 · Cited by 1,199 · see citing works

Cancer Epigenetics: Tumor Heterogeneity, Plasticity of Stem-like States, and Drug Resistance

Easwaran, H., Tsai, H.-C., & Baylin, S. B. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.015 · Cited by 915 · see citing works

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

Teschendorff, A. E., Menon, U., Gentry-Maharaj, A., Ramus, S. J., Weisenberger, D. J., Shen, H., Campan, M., Noushmehr, H., Bell, C. G., Maxwell, A. P., et al. (2010) · Genome Research · doi:10.1101/gr.103606.109 · Cited by 855 · see citing works

Reduced H3K27me3 and DNA Hypomethylation Are Major Drivers of Gene Expression in K27M Mutant Pediatric High-Grade Gliomas

Bender, S., Tang, Y., Lindroth, A. M., Hovestadt, V., Jones, D. T. W., Kool, M., Zapatka, M., Northcott, P. A., Sturm, D., Wang, W., et al. (2013) · Cancer Cell · doi:10.1016/j.ccr.2013.10.006 · Cited by 818 · see citing works

DNA Methylation in Cancer and Aging

Klutstein, M., Nejman, D., Greenfield, R., & Cedar, H. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-3278 · Cited by 810 · see citing works

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells

Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., Klugman, S., et al. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.03.018 · Cited by 806 · see citing works

SDH mutations establish a hypermethylator phenotype in paraganglioma

Letouzé, E., Martinelli, C., Loriot, C., Burnichon, N., Abermil, N., Ottolenghi, C., Janin, M., Menara, M., Nguyen, A. T., Benit, P., et al. (2013) · Cancer Cell · doi:10.1016/j.ccr.2013.04.018 · Cited by 776 · see citing works

Epigenetic gene silencing in cancer: the DNA hypermethylome

Esteller, M. (2007) · Human Molecular Genetics · doi:10.1093/hmg/ddm018 · Cited by 725 · see citing works

Metabolic Regulation of Epigenetics

Lu, C., & Thompson, C. B. (2012) · Cell Metabolism · doi:10.1016/j.cmet.2012.06.001 · Cited by 699 · see citing works

The intestinal stem cell

Barker, N., van de Wetering, M., & Clevers, H. (2008) · Genes & Development · doi:10.1101/gad.1674008 · Cited by 629 · see citing works

The roles of DNA, RNA and histone methylation in ageing and cancer

Michalak, E. M., Burr, M. L., Bannister, A. J., & Dawson, M. A. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0143-1 · Cited by 549 · see citing works

Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures

Plaisier, S. B., Taschereau, R., Wong, J. A., & Graeber, T. G. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq636 · Cited by 468 · see citing works

The emerging role of epigenetic therapeutics in immuno-oncology

Topper, M. J., Vaz, M., Marrone, K. A., Brahmer, J. R., & Baylin, S. B. (2020) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-019-0266-5 · Cited by 433 · see citing works

The putative cancer stem cell marker USP22 is a subunit of the human SAGA complex required for activated transcription and cell-cycle progression

Zhang, X.-Y., Varthi, M., Sykes, S. M., Phillips, C., Warzecha, C., Zhu, W., Wyce, A., Thorne, A. W., Berger, S. L., & McMahon, S. B. (2008) · Molecular Cell · doi:10.1016/j.molcel.2007.12.015 · Cited by 427 · see citing works

Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas

Wang, P., Dong, Q., Zhang, C., Kuan, P.-F., Liu, Y., Jeck, W. R., Andersen, J. B., Jiang, W., Savich, G. L., Tan, T.-X., et al. (2013) · Oncogene · doi:10.1038/onc.2012.315 · Cited by 399 · see citing works

Double Strand Breaks Can Initiate Gene Silencing and SIRT1-Dependent Onset of DNA Methylation in an Exogenous Promoter CpG Island

O'Hagan, H. M., Mohammad, H. P., & Baylin, S. B. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000155 · Cited by 386 · see citing works

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

Zhang, S., Liu, C.-C., Li, W., Shen, H., Laird, P. W., & Zhou, X. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks725 · Cited by 374 · see citing works

Chromatin repressive complexes in stem cells, development, and cancer

Laugesen, A., & Helin, K. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.05.006 · Cited by 352 · see citing works

Environmental epigenetics: prospects for studying epigenetic mediation of exposure–response relationships

Cortessis, V. K., Thomas, D. C., Levine, A. J., Breton, C. V., Mack, T. M., Siegmund, K. D., Haile, R. W., & Laird, P. W. (2012) · Human Genetics · doi:10.1007/s00439-012-1189-8 · Cited by 319 · see citing works

Poised epigenetic states and acquired drug resistance in cancer

Brown, R., Curry, E., Magnani, L., Wilhelm-Benartzi, C. S., & Borley, J. (2014) · Nature Reviews Cancer · doi:10.1038/nrc3819 · Cited by 301 · see citing works

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

Smith, Z. D., Shi, J., Gu, H., Donaghey, J., Clement, K., Cacchiarelli, D., Gnirke, A., Michor, F., & Meissner, A. (2017) · Nature · doi:10.1038/nature23891 · Cited by 201 · see citing works

Epigenetic regulation of the<i>INK4b-ARF-INK4a</i>locus: In sickness and in health

Popov, N., & Gil, J. (2010) · Epigenetics · doi:10.4161/epi.5.8.12996 · Cited by 202 · see citing works

Characterizing DNA methylation alterations from The Cancer Genome Atlas

Weisenberger, D. J. (2014) · Journal of Clinical Investigation · doi:10.1172/jci69740 · Cited by 200 · see citing works

Epigenetic alterations in autoimmune rheumatic diseases

Ballestar, E. (2011) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2011.16 · Cited by 173 · see citing works

Epigenetic cancer therapy: rationales, targets and drugs

Rius, M., & Lyko, F. (2012) · Oncogene · doi:10.1038/onc.2011.601 · Cited by 157 · see citing works

Histone H3.3K27M Represses <i>p16</i> to Accelerate Gliomagenesis in a Murine Model of DIPG

Cordero, F. J., Huang, Z., Grenier, C., He, X., Hu, G., McLendon, R. E., Murphy, S. K., Hashizume, R., & Becher, O. J. (2017) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-16-0389 · Cited by 157 · see citing works

A Comprehensive Microarray-Based DNA Methylation Study of 367 Hematological Neoplasms

Martin-Subero, J. I., Ammerpohl, O., Bibikova, M., Wickham-Garcia, E., Agirre, X., Alvarez, S., Brüggemann, M., Bug, S., Calasanz, M. J., Deckert, M., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006986 · Cited by 134 · see citing works

DNA Methylation Patterns Separate Senescence from Transformation Potential and Indicate Cancer Risk

Xie, W., Kagiampakis, I., Pan, L., Zhang, Y. W., Murphy, L., Tao, Y., Kong, X., Kang, B., Xia, L., Carvalho, F. L. F., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.01.008 · Cited by 122 · see citing works

Transcriptional regulation of cellular senescence

Lanigan, F., Geraghty, J. G., & Bracken, A. P. (2011) · Oncogene · doi:10.1038/onc.2011.34 · Cited by 95 · see citing works

Targeting of EZH2 to a defined genomic site is sufficient for recruitment of Dnmt3a but not de novo DNA methylation

Rush, M., Appanah, R., Lee, S., Lam, L. L., Goyal, P., & Lorincz, M. C. (2009) · Epigenetics · doi:10.4161/epi.4.6.9392 · Cited by 83 · see citing works

Polycomb proteins in hematologic malignancies

Martin-Perez, D., Piris, M. A., & Sanchez-Beato, M. (2010) · Blood · doi:10.1182/blood-2010-05-267096 · Cited by 65 · see citing works

Methylation-Based Therapies for Colorectal Cancer

Cervena, K., Siskova, A., Buchler, T., Vodicka, P., & Vymetalkova, V. (2020) · Cells · doi:10.3390/cells9061540 · Cited by 57 · see citing works

Immortality, but not oncogenic transformation, of primary human cells leads to epigenetic reprogramming of DNA methylation and gene expression

Gordon, K., Clouaire, T., Bao, X. X., Kemp, S. E., Xenophontos, M., de Las Heras, J. I., & Stancheva, I. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1351 · Cited by 44 · see citing works

The Polycomb Group Protein Regulatory Network

Mozgová, I., & Hennig, L. (2015) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-043014-115627 · Cited by 306 · see citing works

Epigenetic inheritance of expression states in plant development: the role of Polycomb group proteins

Köhler, C., & Grossniklaus, U. (2002) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(02)00394-0 · Cited by 63 · see citing works

Polycomb Repression under the Skin

Pirrotta, V. (2009) · Cell · doi:10.1016/j.cell.2009.03.004 · Cited by 4 · see citing works

Histone H2A monoubiquitination and Polycomb repression

Scheuermann, J. C., Gutiérrez, L., & Müller, J. (2012) · Fly · doi:10.4161/fly.20986 · Cited by 50 · see citing works

De novo recruitment of Polycomb-group proteins in Drosophila embryos

Abed, J. A., Ghotbi, E., Ye, P., Frolov, A., Benes, J. J., & Jones, R. S. (2018) · Development · doi:10.1242/dev.165027 · Cited by 14 · see citing works