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Polyamine analogs modulate gene expression by inhibiting lysine-specific demethylase 1 (LSD1) and altering chromatin structure in human breast cancer cells

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Abstract

Aberrant epigenetic repression of gene expression has been implicated in most cancers, including breast cancer. The nuclear amine oxidase, lysine-specific demethylase 1 (LSD1) has the ability to broadly repress gene expression by removing the activating mono- and di-methylation marks at the lysine 4 residue of histone 3 (H3K4me1 and me2). Additionally, LSD1 is highly expressed in estrogen receptor α negative (ER−) breast cancer cells. Since epigenetic marks are reversible, they make attractive therapeutic targets. Here we examine the effects of polyamine analog inhibitors of LSD1 on gene expression, with the goal of targeting LSD1 as a therapeutic modality in the treatment of breast cancer. Exposure of the ER-negative human breast cancer cells, MDA-MB-231 to the LSD1 inhibitors, 2d or PG11144, significantly increases global H3K4me1 and H3K4me2, and alters gene expression. Array analysis indicated that 98 (75 up and 23 down) and 477 (237 up and 240 down) genes changed expression by at least 1.5-fold or greater after treatment with 2d and PG11144, respectively. The expression of 12 up-regulated genes by 2d and 14 up-regulated genes by PG11144 was validated by quantitative RT-PCR. Quantitative chromatin immunoprecipitation (ChIP) analysis demonstrated that up-regulated gene expression by polyamine analogs is associated with increase of the active histone marks H3K4me1, H3K4me2 and H3K9act, and decrease of the repressive histone marks H3K9me2 and H3K27me3, in the promoter regions of the relevant target genes. These data indicate that the pharmacologic inhibition of LSD1 can effectively alter gene expression and that this therapeutic strategy has potential.

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Abbreviations

Aza:

5-Azacytidine

LSD1:

Lysine-specific demethylase 1

DNMT:

DNA methyltransferase

GAPDH:

Glyceraldehyde 3-phosphate dehydrogenase

HDAC:

Histone deacetylase

ODC:

Ornithine decarboxylasae

H3K4:

Lysine 4 of histone 3

H3K9act:

Acetylated lysine 9 of histone 3

H3K27:

Lysine 27 of histone 3

me1:

Monomethyl

me2:

Dimethyl

me3:

Trimethyl

ChIP:

Chromatin immunoprecipitation

mt1f:

Metallothionein 1F

nupr:

Nuclear protein/transcription regulator 1

egr1:

Early growth response 1

cdh16:

Cadherin 16/KSP-cadherin

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Acknowledgments

This work was funded by NIH grants CA51085, CA98454, and CA149095, Susan G. Komen for the Cure KG088923, and the Samuel Waxman Cancer Research Foundation.

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Authors and Affiliations

  1. The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA

    Qingsong Zhu & Robert A. Casero Jr.

  2. Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15232, USA

    Yi Huang & Nancy E. Davidson

  3. Department of Laboratory Medicine, The University of California, San Francisco School of Medicine, San Francisco, CA, 94143, USA

    Laurence J. Marton

  4. Department of Pharmaceutical and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA

    Patrick M. Woster

  5. Department of Oncology, Johns Hopkins University, Bunting-Blaustein Cancer Research Building 1, Room 551, 1650 Orleans Street, Baltimore, MD, 21231, USA

    Robert A. Casero Jr.

Authors
  1. Qingsong Zhu
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  2. Yi Huang
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  3. Laurence J. Marton
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  4. Patrick M. Woster
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  5. Nancy E. Davidson
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  6. Robert A. Casero Jr.
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Correspondence to Robert A. Casero Jr..

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726_2011_1004_MOESM1_ESM.pdf

Fig. S1. Representative gene networks altered by 2d or PG11144. The networks altered by 2d corresponds functionally to cell death, gene expression and carbohydrate metabolism (A); cell cycle, cellular growth and proliferation and cell death (B); cellular growth and proliferation, hematological system development and function, inflammatory response (C). PG11144 changes lipid metabolism, small molecule biochemistry, vitamin and mineral metabolism (D); cell cycle, nutritional disease, cardiovascular disease (E); cancer, cell cycle and cellular movement networks (F). Supplementary material 1 (PDF 349 kb)

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Zhu, Q., Huang, Y., Marton, L.J. et al. Polyamine analogs modulate gene expression by inhibiting lysine-specific demethylase 1 (LSD1) and altering chromatin structure in human breast cancer cells. Amino Acids 42, 887–898 (2012). https://doi.org/10.1007/s00726-011-1004-1

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