The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns
Open accessAbstract
Introduction: Five different molecular subtypes of breast cancer have been identified through gene expression profiling. Each subtype has a characteristic expression pattern suggested to partly depend on cellular origin. We aimed to investigate whether the molecular subtypes also display distinct methylation profiles. Methods: We analysed methylation status of 807 cancer-related genes in 189 fresh frozen primary breast tumours and four normal breast tissue samples using an array-based methylation assay. Results: Unsupervised analysis revealed three groups of breast cancer with characteristic methylation patterns. The three groups were associated with the luminal A, luminal B and basal-like molecular subtypes of breast cancer, respectively, whereas cancers of the HER2-enriched and normal-like subtypes were distributed among the three groups. The methylation frequencies were significantly different between subtypes, with luminal B and basal-like tumours being most and least frequently methylated, respectively. Moreover, targets of the polycomb repressor complex in breast cancer and embryonic stem cells were more methylated in luminal B tumours than in other tumours. BRCA2-mutated tumours had a particularly high degree of methylation. Finally, by utilizing gene expression data, we observed that a large fraction of genes reported as having subtype-specific expression patterns might be regulated through methylation. Conclusions: We have found that breast cancers of the basal-like, luminal A and luminal B molecular subtypes harbour specific methylation profiles. Our results suggest that methylation may play an important role in the development of breast cancers.
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Cites
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288
Jaenisch, R., & Bird, A. (2003) · Nature Genetics · doi:10.1038/ng1089 · Cited by 6,325
TM4: a free, open-source system for microarray data management and analysis
Saeed, A. I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T., Thiagarajan, M., et al. (2003) · BioTechniques · doi:10.2144/03342mt01 · Cited by 4,837
kConFab, Lim, E., Vaillant, F., Wu, D., Forrest, N. C., Pal, B., Hart, A. H., Asselin-Labat, M.-L., Gyorki, D. E., Ward, T., et al. (2009) · Nature Medicine · doi:10.1038/nm.2000 · Cited by 1,492 · cited 2×
“Moreover, polycomb proteins such as EZH2 are involved in stem cell maintenance [6], in line with findings that basal-like breast cancer has a more stem cell-like phenotype [21,41].”
Schlesinger, Y., Straussman, R., Keshet, I., Farkash, S., Hecht, M., Zimmerman, J., Eden, E., Yakhini, Z., Ben-Shushan, E., Reubinoff, B. E., et al. (2007) · Nature Genetics · doi:10.1038/ng1950 · Cited by 1,226 · cited 3×
“Alternatively, polycomb-mediated methylation of H3K27 could function as a mark of sequences for de novo methylation of CpG islands in cancer cells [9,11,43].”
Epigenetic stem cell signature in cancer
Widschwendter, M., Fiegl, H., Egle, D., Mueller-Holzner, E., Spizzo, G., Marth, C., Weisenberger, D. J., Campan, M., Young, J., Jacobs, I., et al. (2007) · Nature Genetics · doi:10.1038/ng1941 · Cited by 1,143
Ohm, J. E., McGarvey, K. M., Yu, X., Cheng, L., Schuebel, K. E., Cope, L., Mohammad, H. P., Chen, W., Daniel, V. C., Yu, W., et al. (2007) · Nature Genetics · doi:10.1038/ng1972 · Cited by 1,130
Tan, J., Yang, X., Zhuang, L., Jiang, X., Chen, W., Lee, P. L., Karuturi, R. K. M., Tan, P. B. O., Liu, E. T., & Yu, Q. (2007) · Genes & Development · doi:10.1101/gad.1524107 · Cited by 895 · cited 3×
“[31], and present in our gene expression data set or methylation panel, respectively, were used.”
InfluentialPolycomb Group Protein Ezh2 Controls Actin Polymerization and Cell Signaling
Su, I.-H., Dobenecker, M.-W., Dickinson, E., Oser, M., Basavaraj, A., Marqueron, R., Viale, A., Reinberg, D., Wülfing, C., & Tarakhovsky, A. (2005) · Cell · doi:10.1016/j.cell.2005.02.029 · Cited by 365
Cited by
MYC-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis
Terunuma, A., Putluri, N., Mishra, P., Mathé, E. A., Dorsey, T. H., Yi, M., Wallace, T. A., Issaq, H. J., Zhou, M., Killian, J. K., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci71180 · Cited by 428
Guillen, K. P., Fujita, M., Butterfield, A. J., Scherer, S. D., Bailey, M. H., Chu, Z., DeRose, Y. S., Zhao, L., Cortes-Sanchez, E., Yang, C.-H., et al. (2022) · Nature Cancer · doi:10.1038/s43018-022-00337-6 · Cited by 416
Balko, J. M., Cook, R. S., Vaught, D. B., Kuba, M. G., Miller, T. W., Bhola, N. E., Sanders, M. E., Granja-Ingram, N. M., Smith, J. J., Meszoely, I. M., et al. (2012) · Nature Medicine · doi:10.1038/nm.2795 · Cited by 262
Miyake, T., Nakayama, T., Naoi, Y., Yamamoto, N., Otani, Y., Kim, S. J., Shimazu, K., Shimomura, A., Maruyama, N., Tamaki, Y., et al. (2012) · Cancer Science · doi:10.1111/j.1349-7006.2012.02231.x · Cited by 146
Rydén, L., Loman, N., Larsson, C., Hegardt, C., Vallon-Christersson, J., Malmberg, M., Lindman, H., Ehinger, A., Saal, L. H., & Borg, Å. (2018) · British Journal of Surgery · doi:10.1002/bjs.10741 · Cited by 62
Self-citation
Metadata
- Authors
- Holm, K., Hegardt, C., Staaf, J., Vallon-Christersson, J., Jönsson, G., Olsson, H., Borg, Å., & Ringnér, M.
- Venue
- Breast Cancer Research
- Published
- 2010-06-18
- Volume
- 12
- Issue
- 3
- Pages
- R36-R36
- ISSN
- 1465-5411 (ISSN-L)
- 1465-542X
- OpenAlex
- W2147944526
- Cited by
- 309
- References
- 9
- FWCI
- 9.10
- Type
- journal article
- Language
- en
- Open access
- gold
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