User menu

DNA methylation profiling reveals a predominant immune component in breast cancers.

Bibliographic reference Dedeurwaerder, Sarah ; Desmedt, Christine ; Calonne, Emilie ; Singhal, Sandeep K ; Haibe-Kains, Benjamin ; et. al. DNA methylation profiling reveals a predominant immune component in breast cancers.. In: EMBO Molecular Medicine, Vol. 3, no.12, p. 726-41 (2011)
Permanent URL http://hdl.handle.net/2078.1/124066
  1. Bediaga Naiara G, Acha-Sagredo Amelia, Guerra Isabel, Viguri Amparo, Albaina Carmen, Ruiz Diaz Irune, Rezola Ricardo, Alberdi María Jesus, Dopazo Joaquín, Montaner David, de Renobales Mertxe, Fernández Agustín F, Field John K, Fraga Mario F, Liloglou Triantafillos, de Pancorbo Marian M, DNA methylation epigenotypes in breast cancer molecular subtypes, 10.1186/bcr2721
  2. Bibikova Marina, Le Jennie, Barnes Bret, Saedinia-Melnyk Shadi, Zhou Lixin, Shen Richard, Gunderson Kevin L, Genome-wide DNA methylation profiling using Infinium®assay, 10.2217/epi.09.14
  3. Bock C., Reither S., Mikeska T., Paulsen M., Walter J., Lengauer T., BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing, 10.1093/bioinformatics/bti652
  4. Bock Christoph, Walter Jörn, Paulsen Martina, Lengauer Thomas, CpG Island Mapping by Epigenome Prediction, 10.1371/journal.pcbi.0030110
  5. Denkert Carsten, Loibl Sibylle, Noske Aurelia, Roller Marc, Müller Berit Maria, Komor Martina, Budczies Jan, Darb-Esfahani Silvia, Kronenwett Ralf, Hanusch Claus, von Törne Christian, Weichert Wilko, Engels Knut, Solbach Christine, Schrader Iris, Dietel Manfred, von Minckwitz Gunter, Tumor-Associated Lymphocytes As an Independent Predictor of Response to Neoadjuvant Chemotherapy in Breast Cancer, 10.1200/jco.2009.23.7370
  6. Desmedt C., Haibe-Kains B., Wirapati P., Buyse M., Larsimont D., Bontempi G., Delorenzi M., Piccart M., Sotiriou C., Biological Processes Associated with Breast Cancer Clinical Outcome Depend on the Molecular Subtypes, 10.1158/1078-0432.ccr-07-4756
  7. Fang F., Turcan S., Rimner A., Kaufman A., Giri D., Morris L. G. T., Shen R., Seshan V., Mo Q., Heguy A., Baylin S. B., Ahuja N., Viale A., Massague J., Norton L., Vahdat L. T., Moynahan M. E., Chan T. A., Breast Cancer Methylomes Establish an Epigenomic Foundation for Metastasis, 10.1126/scitranslmed.3001875
  8. Feinberg Andrew P., Phenotypic plasticity and the epigenetics of human disease, 10.1038/nature05919
  9. Ferlay Jacques, Shin Hai-Rim, Bray Freddie, Forman David, Mathers Colin, Parkin Donald Maxwell, Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008, 10.1002/ijc.25516
  10. Flanagan James M., Cocciardi Sibylle, Waddell Nic, Johnstone Cameron N., Marsh Anna, Henderson Stephen, Simpson Peter, da Silva Leonard, Khanna Kumkum, Lakhani Sunil, Boshoff Chris, Chenevix-Trench Georgia, DNA Methylome of Familial Breast Cancer Identifies Distinct Profiles Defined by Mutation Status, 10.1016/j.ajhg.2010.02.008
  11. Holm Karolina, Hegardt Cecilia, Staaf Johan, Vallon-Christersson Johan, Jönsson Göran, Olsson Håkan, Borg Åke, Ringnér Markus, Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns, 10.1186/bcr2590
  12. Irizarry Rafael A, Ladd-Acosta Christine, Wen Bo, Wu Zhijin, Montano Carolina, Onyango Patrick, Cui Hengmi, Gabo Kevin, Rongione Michael, Webster Maree, Ji Hong, Potash James B, Sabunciyan Sarven, Feinberg Andrew P, The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores, 10.1038/ng.298
  13. Jones Peter A., Baylin Stephen B., The Epigenomics of Cancer, 10.1016/j.cell.2007.01.029
  14. Laird Peter W., Early detection: The power and the promise of DNA methylation markers, 10.1038/nrc1045
  15. Liedtke Cornelia, Hatzis Christos, Symmans William Fraser, Desmedt Christine, Haibe-Kains Benjamin, Valero Vicente, Kuerer Henry, Hortobagyi Gabriel N., Piccart-Gebhart Martine, Sotiriou Christos, Pusztai Lajos, Genomic Grade Index Is Associated With Response to Chemotherapy in Patients With Breast Cancer, 10.1200/jco.2008.18.5934
  16. Lim Elgene, Vaillant François, Wu Di, Forrest Natasha C, Pal Bhupinder, Hart Adam H, Asselin-Labat Marie-Liesse, Gyorki David E, Ward Teresa, Partanen Audrey, Feleppa Frank, Huschtscha Lily I, Thorne Heather J, Fox Stephen B, Yan Max, French Juliet D, Brown Melissa A, Smyth Gordon K, Visvader Jane E, Lindeman Geoffrey J, Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers, 10.1038/nm.2000
  17. Lusa Lara, McShane Lisa M., Reid James F., De Cecco Loris, Ambrogi Federico, Biganzoli Elia, Gariboldi Manuela, Pierotti Marco A., Challenges in Projecting Clustering Results Across Gene Expression–Profiling Datasets, 10.1093/jnci/djm216
  18. Pathiraja Thushangi N., Stearns Vered, Oesterreich Steffi, Epigenetic Regulation in Estrogen Receptor Positive Breast Cancer—Role in Treatment Response, 10.1007/s10911-010-9166-0
  19. Perou Charles M., Sørlie Therese, Eisen Michael B., van de Rijn Matt, Jeffrey Stefanie S., Rees Christian A., Pollack Jonathan R., Ross Douglas T., Johnsen Hilde, Akslen Lars A., Fluge Øystein, Pergamenschikov Alexander, Williams Cheryl, Zhu Shirley X., Lønning Per E., Børresen-Dale Anne-Lise, Brown Patrick O., Botstein David, 10.1038/35021093
  20. Prat Aleix, Perou Charles M., Mammary development meets cancer genomics, 10.1038/nm0809-842
  21. Rønneberg Jo Anders, Fleischer Thomas, Solvang Hiroko Kato, Nordgard Silje H., Edvardsen Hege, Potapenko Ivan, Nebdal Daniel, Daviaud Christian, Gut Ivo, Bukholm Ida, Naume Bjørn, Børresen-Dale Anne-Lise, Tost Jörg, Kristensen Vessela, Methylation profiling with a panel of cancer related genes: Association with estrogen receptor, TP53 mutation status and expression subtypes in sporadic breast cancer, 10.1016/j.molonc.2010.11.004
  22. Salmond Robert J., Filby Andrew, Qureshi Ihjaaz, Caserta Stefano, Zamoyska Rose, T-cell receptor proximal signaling via the Src-family kinases, Lck and Fyn, influences T-cell activation, differentiation, and tolerance, 10.1111/j.1600-065x.2008.00745.x
  23. Sorlie T., Perou C. M., Tibshirani R., Aas T., Geisler S., Johnsen H., Hastie T., Eisen M. B., van de Rijn M., Jeffrey S. S., Thorsen T., Quist H., Matese J. C., Brown P. O., Botstein D., Lonning P. E., Borresen-Dale A.-L., Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications, 10.1073/pnas.191367098
  24. Sorlie T., Tibshirani R., Parker J., Hastie T., Marron J. S., Nobel A., Deng S., Johnsen H., Pesich R., Geisler S., Demeter J., Perou C. M., Lonning P. E., Brown P. O., Borresen-Dale A.-L., Botstein D., Repeated observation of breast tumor subtypes in independent gene expression data sets, 10.1073/pnas.0932692100
  25. Sotiriou Christos, Piccart Martine J., Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care?, 10.1038/nrc2173
  26. Sotiriou Christos, Pusztai Lajos, Gene-Expression Signatures in Breast Cancer, 10.1056/nejmra0801289
  27. Sotiriou C., Neo S.-Y., McShane L. M., Korn E. L., Long P. M., Jazaeri A., Martiat P., Fox S. B., Harris A. L., Liu E. T., Breast cancer classification and prognosis based on gene expression profiles from a population-based study, 10.1073/pnas.1732912100
  28. Stingl John, Caldas Carlos, Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis, 10.1038/nrc2212
  29. Sun Zhifu, Asmann Yan W., Kalari Krishna R., Bot Brian, Eckel-Passow Jeanette E., Baker Tiffany R., Carr Jennifer M., Khrebtukova Irina, Luo Shujun, Zhang Lu, Schroth Gary P., Perez Edith A., Thompson E. Aubrey, Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing, 10.1371/journal.pone.0017490
  30. Van der Auwera Ilse, Yu Wayne, Suo Liping, Van Neste Leander, van Dam Peter, Van Marck Eric A., Pauwels Patrick, Vermeulen Peter B., Dirix Luc Y., Van Laere Steven J., Array-Based DNA Methylation Profiling for Breast Cancer Subtype Discrimination, 10.1371/journal.pone.0012616
  31. van 't Veer Laura J., Dai Hongyue, van de Vijver Marc J., He Yudong D., Hart Augustinus A. M., Mao Mao, Peterse Hans L., van der Kooy Karin, Marton Matthew J., Witteveen Anke T., Schreiber George J., Kerkhoven Ron M., Roberts Chris, Linsley Peter S., Bernards René, Friend Stephen H., Gene expression profiling predicts clinical outcome of breast cancer, 10.1038/415530a
  32. Visvader Jane E., Keeping abreast of the mammary epithelial hierarchy and breast tumorigenesis, 10.1101/gad.1849509
  33. Weber Michael, Hellmann Ines, Stadler Michael B, Ramos Liliana, Pääbo Svante, Rebhan Michael, Schübeler Dirk, Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome, 10.1038/ng1990
  34. Wirapati Pratyaksha, Sotiriou Christos, Kunkel Susanne, Farmer Pierre, Pradervand Sylvain, Haibe-Kains Benjamin, Desmedt Christine, Ignatiadis Michail, Sengstag Thierry, Schütz Frédéric, Goldstein Darlene R, Piccart Martine, Delorenzi Mauro, Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures, 10.1186/bcr2124
  35. Wu Jiansheng, Katrekar Anjali, Honigberg Lee A., Smith Ashley M., Conn Marion T., Tang Jie, Jeffery Doug, Mortara Kyle, Sampang Jun, Williams Steve R., Buggy Joseph, Clark James M., Identification of Substrates of Human Protein-tyrosine Phosphatase PTPN22, 10.1074/jbc.m600498200