Diet and Epigenetics

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Diet and Epigenetics

• Sharon Ross

Nutritional Science Research Group Division of
Cancer Prevention National Cancer
Institute Bethesda, MD 20892
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Epigenetic Regulation of Cancer
Global Hypomethylation
Epigenetics Regulates Cell Cycle Control DNA
Damage Apoptosis Invasion X-Chromosome
Inactivation Imprinting Aging
Site Specific Hypermethylation
Regulating Factors Dietary Hormonal Genetic
Histone Modifications
DNA Methyltransferases Histone Methyltransferases
Histone Acetylases/Deacetylases
Verma M, Srivastava S. Lancet Oncol. (2002)
3755-63.
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DNA
SAM
MAT
DNA
PE
dietary folates
PEMT
methylated-DNA
dTMP
PC
choline
DHF
DMG
methionine
SAH
CDP-choline
dUMP
BHMT
Ach
betaine
THF
ser
choline-P
MS
(B6)
gly
(B12)
5,10-MTHF
homocysteine
MTHFR
-
CBS
5-MTHF
SAM
(B6)

cystathionine
SAM
dietary folates
cysteine
GSH
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Bioactive Food Components in Epigenetic Processes
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LTR Hypomethylated
LTR Hypermethylated
Maternal Supplements with zinc methionine choline
folate B12
Yellow Mouse
Agouti Mouse

• Lower risk of cancer, diabetes, obesity
• Prolonged life

• High risk cancer, diabetes, obesity
• Reduced lifespan

Cooney et al. (2002) J Nutr. 1322393S
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Prevalence of promoter methylation for high and
low methyl intake (classified by alcohol and
folate intake)
n61 van Engeland et al. Cancer
Research 63 3133-3137, 2003
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Tea Polyphenol Epigallocatechin-3-Gallate
Inhibits DNA Methyltransferase Activity
Fang et al. Cancer Res. 63(22) 2003
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Consequences of Epigallocatechin-3-Gallate
Inhibition of DNA Methyltransferase Activity
Demethylation reversal of hypermethylation of
p16INK4a, RARß, (MGMT), and hMLH1
genes Reactivation increased expression of mRNA
for p16INK4a, RARß, (MGMT), and hMLH1 genes
Fang et al. Cancer Res. 63(22) 2003
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Sensitization by 5-Aza-deoxycytidine of Leukemia
Cells to Differentiation by Retinoic Acid
Untreated Retinoic Acid 5-AZA 5-AZA Retinoic
Acid-
40 -
30 -
Differentiation Ratio
20 -
10 -
SN-1
KOCL33
KOCL51
Nitsu, et al. British Journal of Hematology 112
315, 2001.
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Dietary Factors Influencing Histone Modifications
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Histone Modifications

• Covalent modification of histones
• Acetylation of lysines
• Methylation of lysines and arginines
• Phosphorylations of serines and threonines
• ADP-ribosylation of glutamic acids
• Ubiquitination of lysine residues
• Sumolyation of lysine residues
• Biotinylation of lysines

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Johnstone 2002Epigenetic Mechanisms
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Chromatin-Level Regulation of Gene Expression
Inactive Chromatin
SFN, DADS
Garfinkel and Ruden Nutrition2056-62, 2004
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Effects of Fatty Acids on Mammalian Cells in
Culture
Davie JR. J. Nutr. 133 2485S-2493S, 2003
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A model for butyrate induction of p21Waf1/Cip1
gene expression and inhibition of cell cycle
Davie JR. J. Nutr. 133 2485S-2493S, 2003
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Sulforaphane inhibits HDAC activity in HCT116
cells
The wedge symbol, 0, 3, 9, 15 µM SFN
Myzak et al. Cancer Research 64 5767-5774, 2004
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Sulforaphane increases histone acetylation and
p21Cip1/Waf1 protein
The wedge symbol, 0, 9, 15 µM SFN
Myzak et al. Cancer Research 64 5767-5774, 2004
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DADS Influences p21waf1/cip1 mRNA and Protein
Levels in HT-29 Cells
Druesne N et al. Carcinogenesis 25 1227-1236,
2004
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Effects of DADS on the acetylation of histones in
HT-29 cells
Druesne N et al. Carcinogenesis 25 1227-1236,
2004
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Chromatin-Level Regulation of Gene Expression
Inactive Chromatin
SFN, DADS
resveratrol
Garfinkel and Ruden Nutrition2056-62, 2004
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Sirtuin 1 (SIRT1) a protein deacetylase

• Mammalian orthologue of the yeast SIR2
• Expression associated with longevity, cell
  survival
• NAD-dependent histone deacetylase
• SIRT1 deacetylates histone polypeptides with a
  preference for histone H4 lysine 16 and H3 lysine
  9 in vitro.
• RNAi-mediated decreased expression of SIRT1 in
  human cells resulted in hyperacetylation of
  H4-K16 and H3-K9 in vivo.
• SIRT1 protein deacetylates non-histone substrates
  (p53, MyoD), as well as histone substrates

Vaquero A, et al. Mol Cell. 1693-105, 2004.
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Caloric restriction increases SIRT1 expression in
a variety of rat tissues
Cohen HY, et al. Science 305390-392, 2004.
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Resveratrol increases NAD-dependent HDAC activity
Yeung F, et al. Embo J. 232369-2380, 2004
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SIRT1-mediated deaceytlation
Yeung F, et al. Embo J. 232369-2380, 2004
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Chromatin-Level Regulation of Gene Expression
SFN, DADS
resveratrol
Garfinkel and Ruden Nutrition2056-62, 2004
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Histone Methyltransferases

• Transfer methyl groups from the methyl donor
  S-adenosylmethionine to the arginine or lysine
  residues in histones or other proteins
• Three classes based on the sequence and structure
  of their catalytic domain protein arginine
  methyltransferases, SET domain containing lysine
  methyltransferases and Dot1 class lysine
  methyltransferases.
• The SET domain family has been linked with
  mitotic inheritance of gene activity and
  carcinogenesis.
• Methylation is among the most stable histone
  modifications.
• The initiation and maintenance of heterochromatin
  is carried out by histone H3 lysine 9
  methylation, whereas euchromatin is characterized
  by H3 lysine 4 methylation.
• Six HMTs methylate H3-K9 (SET domain family)

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Inhibition of histone methylation activity by
increasing SAH levels
Kim K, et al. Cancer Research 637619-7623, 2003
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Chromatin-Level Regulation of Gene Expression
SFN, DADS
resveratrol
Garfinkel and Ruden Nutrition2056-62, 2004
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1,25-Dihydroxyvitamin D(3) Stimulates Cyclic
Vitamin D Receptor/Retinoid X Receptor
DNA-Binding, Co-activator Recruitment, and
Histone Acetylation in Intact Osteoblasts. Kim
S, Shevde NK, Pike JW. J Bone Miner Res. 2005
Feb20(2)305-17. Epub 2004 Nov 16.

• 1,25(OH)(2)D(3) induces rapid association of the
  VDR and RXR with both the Cyp24 and the Opn gene
  promoters in both MC3T3-E1 osteoblasts and MOBs
• 1,25(OH)(2)D(3) treatment also induces rapid
  recruitment of co-regulators such as SRC-1, -2,
  and -3, CBP, and p300 to both promoters
• Recruitment leads to acetylation of histone 4 on
  Cyp24 but not the Opn.

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Histone Acetylation
P.Marks 2001
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P.Marks 2001 Histone
Modification
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Overview of Chromatin-Level Regulation of Gene
Expression
Garfinkel and Ruden Nutrition2056-62, 2004