Epigenetics, nutrition and bowel cancer risk John Mathers

Epigenetics, nutrition and bowel cancer risk John Mathers

Epigenetics, nutrition and bowel
cancer risk
John Mathers
Human Nutrition Research Centre
UK
Diet and bowel cancer risk .1 •  WCRF/ AICR Report •  Comprehensive and systemaEc assessment of epidemiological evidence •  2nd ediEon November 2007 h"p://www.wcrf-­‐uk.org/research_science/expert_report.lasso Colo-­‐rectal cancer .2 Level of
evidence
↓ Risk
↑ Risk
Convincing
Physical activity
Red meat;
processed meat;
alcoholic drinks
(men); abdominal
fat; adult height
Probable
Foods containing dietary
fibre; garlic; milk; calcium
alcoholic drinks
(women)
Limited - suggestive
Vegetables; fruits; folate;
Se; fish; vitamin D
Fe; cheese; animal
fats; sugar
Limited – no
conclusion
Lots
Lots
Substantial effect on
risk unlikely
None identified
None identified
Overview of lecture
  Overview
of epigenetic mechanisms
  Epigenetic events in bowel cancer
  Towards novel diet-related DNA methylation
biomarkers of bowel cancer risk
  MicroRNA, diet and development of bowel cancer
Colon cancer development •  ‘Advantageous’ mutaEons/ epimutaEons become ‘fixed’ •  Development of genomic instability Other geneEc and epigeneEc events •  <10% of adenomas become carcinomas (Darwinian process) Adapted from Rajagopalan et al. (2003) Nat. Rev. Cancer 3, 695-­‐701 Determinants of phenotype Epigenome Environment Adapted from Zoghbi HY & Beaudet AL (2007) in “Epigene2cs” Phenotype The 4 Rs of (nutriConal) epigenomics Environment (diet) Receive and Record Time Mathers JC (2008) Proc. Nutr. Soc. 67, 390-­‐394 Remember Reveal EpigeneCc Mechanisms DNA methylaEon Non-­‐coding RNAs ChromaEn conformaEon Costa FF (2008) Gene 410, 9-­‐17 Histone code EpigeneCc marks DNA methylaEon Histone “decoraEon” Qiu J (2006) Nature 441, 143-­‐145 Molecular mechanisms linking diet with bowel cancer risk All cancers arise from (unrepaired) genomic damage so “protecCve” dietary factors “must”: •  ↓ genomic damage •  ↑ genomic repair •  ↑ removal of damaged cells by apoptosis Hypothesis: aberrant methylaCon of DNA repair genes links diet with cancer Hypothesis: ? InflammaCon Tumour MGMT: role in DNA repair Gerson SL (2004) EpigeneCc events in cancer development – silencing of DNA repair genes Jones PA & Baylin SB (2002) MGMT methylaCon correlates with loss of expression Shen L et al. (2005) J. Natl. Cancer Inst. 97, 1330-­‐1338 ↑ MGMT methylaCon in normal mucosa when adjacent tumour is methylated Causality?
Does aberrant
methylation cause
tumorigenesis?
Shen L et al. (2005) J. Natl. Cancer Inst. 97, 1330-­‐1338 29 genes
often
methylated
in cancer
Tumour
suppressor
genes
Ohm JE et al. (2007)
Nature Genetics 39,
237-242
Genes frequently hypermethylated in
tumours have a stem cell-like
chromatin pattern
Adult
cancers
‘Bivalent’ marks:
Active mark – H3K4
Repressive mark – H3K27
Ohm JE et al. (2007) Nature Genetics 39, 237-242
InterpretaCon of DNA methylaCon measurements Qiu J (2006) Nature 441, 143-­‐145 “Field effect” v. focal event? •  Crypt cells arise from stem cells at base of individual crypts •  Colo-­‐rectal tumours derive from a stem cell in a single crypt •  Nature of “field effect” in vulnerable colon? EpigeneCc “field effect” •  At any CpG, methylaEon is a binary phenomenon •  Percentage methylaEon = % genomes methylated •  Therefore ≈ % stem cells (and crypts) methylated at this locus •  Crypts are epigeneEcally heterogeneous EpigeneCc diversity in colonic mucosa Colo-­‐rectal mucosal crypts: •  MulEple, independent, clonal units •  GeneEcally idenEcal •  EpigeneEcally heterogeneous Why? •  Different local environments? •  StochasCc events? Maintenance of DNA methylaCon pa^erns through mitosis Shibata D (2009) J. Pathol. 217, 199-­‐205 StochasCc development of divergent methylaCon pa^erns ↑ epigeneCc diversity with age (and dietary exposure?) Shibata D (2009) J. Pathol. 217, 199-­‐205 Hypothesis: “Field effects” occur in the “normal” colo-­‐rectal epithelium Young, healthy Older, ↑ CRC risk Similar epigeneEc pa"erns, similar gene expression “High risk” stem cells in individual crypts Stool as a surrogate “Cssue” for DNA methylaCon measurements MethylaCon at specific CpGs (%) QuanCficaCon of gene methylaCon using stool samples Healthy volunteers Belshaw NJ et al. (2004) Cancer Epid. Biomark. Prev. 13, 1495-1501
MethylaCon of promoter region of oestrogen receptor gene ↑ with age in the colon ESR1 methylaCon (%) 200 healthy people in NE England Age (years) Garg D et al. unpublished ↑ promoter methylation in DNA from
stools compared with mucosa
Elliott GO et al. (2010) unpublished
%
*** 40
30
↑ Methylation in stool from adenoma
patients v. healthy volunteers
20
10
0
APC
CDH1
HPP1
ESR1
MLH1
p14
B 80
*** 70
** * 60
% Meth
50
40
*** 30
20
10
0
APC
CDH1
HPP1
ESR1
MLH1
p14
C Healthy
volunteer
80
Adenoma
patient
70
60 (2010) unpublished
Elliott GO et al.
h
50
*** *** *** Stool-­‐based DNA methylaCon measurements •  Human DNA can be harvested from stool •  Quality of DNA is adequate for quanEficaEon of promoter methylaEon •  Some results as anEcipated e.g. age-­‐dependent ↑ in ESR1 methylaEon •  Levels of methylaEon are consistently higher than those seen in corresponding mucosal biopsies •  ? DifferenEal survival of methylated sequences? •  PotenEal use in developing biomarkers of CRC risk “All seeing, all controlling”
Claudia Bentley (2006)
MicroRNA (miRNA)
  Large family of small (≈ 22 nucleotides long) non-coding
RNAs;
  At least 721 miRNA in human genome;
  Regulate transcription of ≈30% of all protein-encoding
genes through sequence-specific binding to RNA;
  Inhibit translation and/or signal degradation of target
mRNA;
  Regulate almost all cellular processes investigated.
Gene regulation
by miRNA
Ryan BM et al. (2010)
Nature Rev. Cancer
10, 389-402
miRNA and cancer
  Some miRNA which are normally “silent” in adult tissues
become re-expressed
Persistent stem cell-like de-differentiated state
  miRNA over-expressed in tumours may act like oncogenes
Oncomirs =
miRNA with a
  miRNA with tumour suppressor (TS) regulatory activity
role
in
cancer
may beome down regulated
↑ proliferation, ↓ apoptosis
loss of TS activity
Jeffrey SS (2008) Nature Biotech. 26, 400-401
Esquela-Kerscher A & Slack FJ (2006) Nature Rev. Cancer 6, 259-269
Anti-cancer
effect of P53
via miRNA
Toledo F & Bardot B (2009)
Nature 460, 466-467
Methylation of miR-34a in tumours
Methylation of
promoter of
miRNA-34a
gene detected
in tumours
including
bowel cancer
Lodygin D et al.
(2008) Cell Cycle 7,
2591-2600
Diet, miRNA and bowel cancer risk
?
  Understanding aetiological mechanisms
  Development of novel diet-responsive biomarkers of
bowel cancer risk
Effect of dietary factors on miRNA
signatures in rat colon
2*2*2 factorial designed study in Sprague-Dawley rats
  2 types of dietary fibre
  2 types of fat
Cellulose
Pectin
Corn oil
Fish oil
  + and – AOM treatment
  Assayed 368 mature miRNAs in colonic mucosa
Davidson LA et al. (2009) Carcinogenesis 30, 2077-2084
Diet alters miRNA in rat colon
Cellulose
Pectin
Corn oil
Fish oil
Davidson LA et
al. (2009)
Carcinogenesis
30, 2077-2084
miRNA patterns linked with
adenocarcinoma risk
Davidson LA et al. (2009) Carcinogenesis 30, 2077-2084
Fish oil “prevented” down regulation
of 5 specific miRNA (oncomirs)
Davidson LA et
al. (2009)
Carcinogenesis
30, 2077-2084
Summary
  Diet is a major modulator of bowel cancer risk
  Epigenetics mechanisms link dietary exposure with
development of bowel cancer
  DNA methylation shows promise as route to novel (dietrelated) biomarkers of bowel cancer risk
  DNA methylation measurements can be made in stool
  Altered miRNA patterns occur in cancer and may be
diet responsive
Research prioriCes •  Which epigeneEc changes in macroscopically normal mucosa are causal for ↑ bowel cancer risk? •  What are major exposures causing ↑ epigeneEc heterogeneity with age? •  What dietary (and other lifestyle) factors prevent, or reverse, these early epigeneEc changes? Acknowledgements Ian Johnson
Nigel Belshaw
Giles Elliott
Mike Bradburn
Dharmendra Garg
Wendy Bal
Liz Williams