Epigenetic Changes Through Airborne Pollutants

Hyang-Min Byun, PhD Research Scientist

Harvard School of Public Health

X X X

X X

1

Clinical Epigenetics Society March 6, 2014

Environment Epigenetics Phenotype

Queen or Worker Diet

GroMaleszka R. 2008 Science.

Temperature Red or White

Shin-Nosuke Hashida 2006 Plant Cell.

How Does Environment Influence Epigenetics?

Fat or Lean Diet

Morgan H.D. 1999 Nat Genet 2

But that doesn’t explain this!

3

http://www.who.int/phe/health_topics/outdoorair/databases/en/index.html 4

Air Pollution Annual Mean by City (based on 2003 to 2010)

5

http://www.who.int/indoorair/en/index.html 6

Air Pollution and Deaths

Biological Pathways of Air Pollution

IL-6

IL-8

TNF

Blood pressure

Blood CRP

ROS generation

Pro-inflammatory signaling

Hypercoagulability

Coronary flow

Disease

• Asthma

• Heart disease

• Neurological disorders

• Lung cancer

• Leukemia

Effects

7

8

circ.ahajournals.org

Black carbon

9

The Size of Particulate Matters of Air Pollutants

Stephen Tonna Nature Reviews Nephrology 2010

DNA methylation

Histone modification

Mitochondrial DNA 10

Epigenetic components

Air pollution Human Cell

X

X X

X X

Adult, Pregnancy, Early life Nuclear Mitochondria DNA Methylation Histone Modifications

Different types of Air Pollutants

Air Pollution and Nuclear DNA Methylation

Air Pollution and Histone Modifications

Air Pollution and Mitochondrial Epigenetics 11

Air Pollution and Nuclear DNA Methylation

12

• Adult • Pregnancy • Early-life

Repetitive Elements (LINE-1 and Alu)

13

Airborne Benzene Exposure and DNA Methylation

• Benzene can be inhaled

• Classified as a human carcinogen

• Benzene is known to cause AML

• Mutagens • Cause aberrant expression of

linked genes • Cause genomic instability • Silenced by DNA methylation

Bollati V et al., Cancer Res. 2007

Bollati V et al., Cancer Res. 2007

LINE-1 Alu

14

Airborne Benzene Exposure and DNA Methylation

1 mya 5 mya 10 mya 15 mya 20 mya 30 mya 40 mya

LINE1-PA5 LINE1-PA2

LINE1-HS

LINE1-TA

Alu-Sx

Alu-Ya8

Alu-d6 15

LINE1 and Alu Subfamily by Evolutionary Age

DNA Methylation level and Evolutionary Age

LINE1-Ta

Alu-Yb8

Alu-Yd6

LINE1-Hs

LINE1-PA2

LINE1-PA5 Alu-Sx

0

20

40

60

80

100

0 5 10 15 20 25 30 35 40 45

% D

NA

me

thy

lati

on

Age (Mya)

16 Byun HM et al., Part Fibre Toxicol 2013

Study 1 Foundry workers PM10

17

Specificity of LINE1 and Alu Subfamily

Study 2 Gas-station attendants Benzene

LINE-1 Subfamily and Air pollution

-3.0

-2.5

-2.0

-1.5

-1.0

-0.5

0.0

0.5

4.2 57.0 109.7 162.5

26111520

Air benzene exposure (μg/m3)

Mya

p=0.045

Study 2 (Air benzene)

-3.0

-2.5

-2.0

-1.5

-1.0

-0.5

0.0

0.5

73.7 120.0 166.2 212.4

26111520

PM10 exposure (μg/m3)

Mya

LIN

E-1

DN

A m

eth

yla

tio

n (τ)

p=0.003

Study 1 (PM10)

LIN

E-1

DN

A m

eth

yla

tio

n (τ)

Byun HM et al., Part Fibre Toxicol 2013 18

Alu Subfamily and Air pollution

-3.0

-2.5

-2.0

-1.5

-1.0

-0.5

0.0

0.5

73.7 120.0 166.2 212.4

2015116

Alu

DN

A m

eth

yla

tion

(τ)

p=0.017

Mya

Study 1 (PM10)

PM10 exposure (μg/m3)

Byun HM et al., Part Fibre Toxicol 2013 19

Byun HM et al., Am J Respir Crit Care Med. 2009

• Persistent Asthma in Childhood • Childhood obesity • Metabolic Disorders • Hypertension • Cardiovascular disease • Child cancers

Repetitive Elements: LINE1 and AluYb8

Gene-specific methylation: Illumina methylation array

20

Prenatal Smoking and Child DNA Methylation

Byun HM et al., Am J Respir Crit Care Med. 2009 21

Prenatal Smoking and Child DNA Methylation: Repetitive Elements

Byun HM et al., Am J Respir Crit Care Med. 2009 22

Prenatal Smoking and Child DNA Methylation: Gene-specific

Breton CV et al., Environ Health Perspect. 2012 23

Early Life Exposure and DNA Methylation

• Asthma • Chronic obstructive pulmonary

disease • Obesity • Metabolic Disorders • Cardiovascular disease

PM2.5 and PM10

iNOS (Nos2A) (inducible Nitric oxide synthase)

• Involved in immune response

• Produces NO as an immune defense

mechanism

• May function in autoimmune disease

Distribution of cumulative average PM2.5 (A) and PM10 (B) (µg/m3) for 940 CHS participants by time period.

Breton CV et al., Environ Health Perspect. 2012 24

Early Life Exposure and DNA Methylation

Breton CV et al., Environ Health Perspect. 2012 25

Early Life Exposure and DNA Methylation

iNOS

26

Air Pollution and Histone Modifications

27

Metal-rich air particles and Histone Markers

Foundry work is associated with high risk of cardiovascular disease

Particulate Matter in metals is more than 10 fold higher than in ambient levels

H3K4me2 and H3K9ac is enriched in particular promoters of transcriptionally active genes.

Cantone L et al., Environ Health Perspect. 2011

28 Cantone L et al., Environ Health Perspect. 2011

H3K4me2 H3K9ac

Metal-rich air particles and Histone Markers

Cantone L et al., Environ Health Perspect. 2011

Metal-rich air particles and global H3K4me2

29

Cantone L et al., Environ Health Perspect. 2011

Metal-rich air particles and global H3K9ac

30

31

Air Pollution and Mitochondrial Epigenetics

Because it contains DNA…??

32

Why Mitochondrial Epigenetics?

• ‘Powerhouse’ of the cell • Sensitive to oxidative damage • Anemia, dementia,

hypertension, obesity, diabetes, neurodegenerative disease, cardiovascular disease etc.

Red blood cell Skin

Lymphocyte Heart /brain

Oocytes

X X X

X X

Cell type

0 few hundred

1,000 5,000

100,000-100,000,000

Mitochondrion

2 to >10,000

mtDNA

33

Cell, Mitochondrion and mtDNA

16,569 2 to more than 10,000

37 435 No No x5

Absent or quite limited x10

~3,000,000,000 2

30,000 >28,000,000

Yes Yes x1

High x1

Size (bp) DNA copies per cell

Genes # of CpGs

Introns Histones

Oxidative stress DNA repair

Mutation rate

Byun HM et al., Human Genetics 2014 34

Mitochondrial and Nuclear DNA

35

Foundry work is associated with high risk of cardiovascular disease

Particulate Matter in metals is more than 10 fold higher than in ambient levels

Metal-rich PM and mtDNA Methylation

Mitochondrial DNA • D-loop (promoter region) • tRNA phenylalanine • 12S rRNA

Byun HM et al., Part Fibre Toxicol 2013

Byun HM et al., Part Fibre Toxicol 2013 36

Metal-rich PM and mtDNA Methylation

Low-exposed Foundry workers

High-exposed Foundry workers

MT-T

F &

MT-R

NR

1

% M

eth

yla

tio

n

0.5

Log (PM1 exposure level) 1.0 1.5 2.0 2.5

1

0

-1

-2

Ch

ange

in

MT-

TF &

MT-

RN

R1

M

eth

ylat

ion

(%

)

P=0.02 for linear effect

Byun HM et al., Part Fibre Toxicol 2013 37

Metal-rich PM and mtDNA Methylation

Byun HM et al., Part Fibre Toxicol 2013 38

Metal-rich PM and mtDNA Methylation

39

Summary and Future directions

Air pollution can affect nuclear DNA methylation

and histone modifications and mitochondrial DNA

methylation.

Air pollution can affect epigenetics at every stage

of the human life cycle

Different regions of the genome display differing

sensitivity to such exposures.

Epigenetic communication between nucleus and

mitochondria; Maternal inheritance of mtDNA

epigenetics

Hyang-Min Byun, PhD hmbyun@hsph.harvard.edu

Thank you!