Cell type-specific DNA methylation patterns in the human breast

Noga Bloushtain-Qimron, Jun Yao, Eric L. Snyder, Michail Shipitsin, Lauren L. Campbell, Sendurai A. Mani, Min Hu, Haiyan Chen, Vadim Ustyansky, Jessica E. Antosiewicz, Pedram Argani, Marc K Halushka, James A. Thomson, Paul Pharoah, Angel Porgador, Saraswati Sukumar, Ramon Parsons, Andrea Richardson, Martha R. Stampfer, Rebecca S. Gelman & 3 others Tatiana Nikolskaya, Yuri Nikolsky, Kornelia Polyak

Research output: Contribution to journalArticle

Abstract

Cellular identity and differentiation are determined by epigenetic programs. The characteristics of these programs in normal human mammary epithelium and their similarity to those in stem cells are unknown. To begin investigating these issues, we analyzed the DNA methylation and gene expression profiles of distinct subpopulations of mammary epithelial cells by using MSDK (methylation-specific digital karyotyping) and SAGE (serial analysis of gene expression). We identified discrete cell-type and differentiation state-specific DNA methylation and gene expression patterns that were maintained in a subset of breast carcinomas and correlated with clinically relevant tumor subtypes. CD44+ cells were the most hypomethylated and highly expressed several transcription factors with known stem cell function including HOXA10 and TCF3. Many of these genes were also hypomethylated in BMP4-treated compared with undifferentiated human embryonic stem (ES) cells that we analyzed by MSDK for comparison. Further highlighting the similarity of epigenetic programs of embryonic and mammary epithelial cells, genes highly expressed in CD44+ relative to more differentiated CD24+ cells were significantly enriched for Suz12 targets in ES cells. The expression of FOXC1, one of the transcription factors hypomethylated and highly expressed in CD44+ cells, induced a progenitor-like phenotype in differentiated mammary epithelial cells. These data suggest that epigenetically controlled transcription factors play a key role in regulating mammary epithelial cell phenotypes and imply similarities among epigenetic programs that define progenitor cell characteristics.

Original languageEnglish (US)
Pages (from-to)14076-14081
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume105
Issue number37
DOIs
StatePublished - Sep 16 2008

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DNA Methylation
Breast
Epithelial Cells
Epigenomics
Karyotyping
Transcription Factors
Stem Cells
Methylation
Phenotype
Gene Expression
Human Mammary Glands
Embryonic Stem Cells
Transcriptome
Genes
Cell Differentiation
Breast Neoplasms
Neoplasms

Keywords

  • Cancer
  • Differentiation
  • Progenitor
  • Stem cell

ASJC Scopus subject areas

  • General

Cite this

Bloushtain-Qimron, N., Yao, J., Snyder, E. L., Shipitsin, M., Campbell, L. L., Mani, S. A., ... Polyak, K. (2008). Cell type-specific DNA methylation patterns in the human breast. Proceedings of the National Academy of Sciences of the United States of America, 105(37), 14076-14081. https://doi.org/10.1073/pnas.0805206105

Cell type-specific DNA methylation patterns in the human breast. / Bloushtain-Qimron, Noga; Yao, Jun; Snyder, Eric L.; Shipitsin, Michail; Campbell, Lauren L.; Mani, Sendurai A.; Hu, Min; Chen, Haiyan; Ustyansky, Vadim; Antosiewicz, Jessica E.; Argani, Pedram; Halushka, Marc K; Thomson, James A.; Pharoah, Paul; Porgador, Angel; Sukumar, Saraswati; Parsons, Ramon; Richardson, Andrea; Stampfer, Martha R.; Gelman, Rebecca S.; Nikolskaya, Tatiana; Nikolsky, Yuri; Polyak, Kornelia.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 37, 16.09.2008, p. 14076-14081.

Research output: Contribution to journalArticle

Bloushtain-Qimron, N, Yao, J, Snyder, EL, Shipitsin, M, Campbell, LL, Mani, SA, Hu, M, Chen, H, Ustyansky, V, Antosiewicz, JE, Argani, P, Halushka, MK, Thomson, JA, Pharoah, P, Porgador, A, Sukumar, S, Parsons, R, Richardson, A, Stampfer, MR, Gelman, RS, Nikolskaya, T, Nikolsky, Y & Polyak, K 2008, 'Cell type-specific DNA methylation patterns in the human breast', Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 37, pp. 14076-14081. https://doi.org/10.1073/pnas.0805206105
Bloushtain-Qimron, Noga ; Yao, Jun ; Snyder, Eric L. ; Shipitsin, Michail ; Campbell, Lauren L. ; Mani, Sendurai A. ; Hu, Min ; Chen, Haiyan ; Ustyansky, Vadim ; Antosiewicz, Jessica E. ; Argani, Pedram ; Halushka, Marc K ; Thomson, James A. ; Pharoah, Paul ; Porgador, Angel ; Sukumar, Saraswati ; Parsons, Ramon ; Richardson, Andrea ; Stampfer, Martha R. ; Gelman, Rebecca S. ; Nikolskaya, Tatiana ; Nikolsky, Yuri ; Polyak, Kornelia. / Cell type-specific DNA methylation patterns in the human breast. In: Proceedings of the National Academy of Sciences of the United States of America. 2008 ; Vol. 105, No. 37. pp. 14076-14081.
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AU - Mani, Sendurai A.

AU - Hu, Min

AU - Chen, Haiyan

AU - Ustyansky, Vadim

AU - Antosiewicz, Jessica E.

AU - Argani, Pedram

AU - Halushka, Marc K

AU - Thomson, James A.

AU - Pharoah, Paul

AU - Porgador, Angel

AU - Sukumar, Saraswati

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AU - Richardson, Andrea

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