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BIOL30001 > lecture 26: epigenetics in human health and disease > Flashcards

lecture 26: epigenetics in human health and disease Flashcards

1
Q

What is epigenetics?

A
  • epigenetic modifications mediate changes in gene expression in the absence of change to underlying DNA sequence
  • “the structural adaptation of chromosomal regions so as to register, signal, or perpetuate altered activity states” (Bird, 2007)
  • chromosome-associated factors that regulate the activity of underlying DNA sequence
  • cellular “memory”/’plastic’ in response to environment
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2
Q

What are epigenetic modifications?

A
  • epigenetic mechanisms are affected by these factors and processes:
    • development (in utero, childhood)
    • environmental chemicals
    • drugs/pharmaceuticals
    • ageing
    • diet
  • health endpoints
    • cancer
    • autoimmune disease
    • mental disorders
    • diabetes
  • DNA methylation
    • methyl group (an epigenetic factor found in some dietary sources) can tag DNA and activate or repress genes)
  • Histone modification
    • the binding of epigenetic factors to histone “tails” alters the extent to which DNA is wrapped around histones and the availability of genes in the DNA to be activated
  • variant histones
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3
Q

What is the histone code?

A
  • “writer” enzymes that catalyse modification
  • “eraser” enzymes that remove modification
  • euchromatin (open)
    • acetylation
    • maybe methylation
    • phosphorylation
  • heterochromatin (closed)
    • lots of methylation
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4
Q

What is DNA methylation?

A
  • occurs primarily at CpG in vertebrates
  • On/Off switch at gene promoters, dimmer at gene enhancers
  • CpG island = dense region of CpG sites
  • most CpG sites (greater than 90%) are dispersed around the genome at low densities
  • methylated CpG site → blocked transcription
  • unmethylated CpG site → transcriptionally competent
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5
Q

In what way is chromatin a dynamic equilibrium?

A
  • open or active euchromatic → closed or inactive heterochromatin
    • DNMTs, HDACs, HMTs, MBPs
    • adding hypermethylated histone tails
    • removing hyperacetylated histone tails
    • adding more methylated CpG
  • other way
    • TETs, HATs, HDMs
    • RNA pol complex can access the gene and transcribe it
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6
Q

What is X-chromosome inactivation?

A
  • all female mammals silence one X chromosome
  • expression of non-coding RNA (Xist)
  • change in histone posttranslational modification
    • elevated H3K9, H3K27 methylation
    • loss of histone acetylation
  • incorporation of variant histone protein
    • macroH2A
  • association of chromatin modifying proteins
    • e.g. MBD, ATRX
  • methylation of CpG islands in DNA
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7
Q

What is spatial heterogeneity?

A
  • 1 genome: 1000s of epigenomes
  • sum total of epigenetic modifications within a cell
  • every cell has a distinct epigenome
  • (cumulative environmental factors)n →
  • genotype →
  • (cumulative stochastic influence)n →
  • all lead to epigenotype → gene expression → phenotype
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8
Q

Is DNA methylation static?

A
  • no it is highly dynamic
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9
Q

What is epigenetics in foetal programming and DOHaD?

A
  • environmental exposure (e.g. diet)
    • sub optimal intrauterine environment
  • stochastic factors
  • genetic and sex specific effects
    • disruption in epigenetic profile
      • changes in gene expression
      • metabolic/endocrine disruption
        • modified tissue function/development
        • foetal programming/maladaption?
          • adverse birth outcome including low birth weight
            • predisposition to early life and adult onset disease (e.g. T2D)
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10
Q

What are DNA methylation platforms?

A
  • genome-wide DNA methylation analysis
    • infinium Human Methylation27 (HM27) and HM450 bead arrays
    • 27,000 CpG sites, 14,500 genes or 486,000 CpG sites - all genes
    • 12 samples/array (~$500/Sample)
    • 450 targets all regions
    • 27 targets promoter regions
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11
Q

How variable is the early human epigenome?

A
  • unsupervised clustering of 27,000 DNA methylation values (HM27) from human placenta across gestation
  • watch this
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12
Q

What is a heatmap of most variable probes (1st vs 3rd trimester)?

A
  • increasing methylation
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13
Q

What does the blood of premature infants show?

A
  • large-scale epigenetic differences
  • analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy
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14
Q

What is DNA methylation and T-development?

A
  • HM450 array analysis
  • HT-12 expression analysis
  • genome-scale profiling reveals a subset of genes regulated by DNA methylation that programme somatic T-cell phenotypes in humans
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15
Q

summary thus far

A
  • clear evidence of highly dynamic early life DNA methylation profile in multiple tissues, both before and after birth
  • overall increase in methylation level and number of variable CpG sites over time in blood and placenta
  • evidence for increasing drift (increasing variance) between individuals over time
    • supports a model of cumulative effects of environmental exposure on epigenetic profile during early life
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16
Q

What is the relationship between epigenetics and the environment?

A
  • the inherent sensitivity of epigenetic processes to subcellular environmental cues, that is a hallmark of differentiation and development, also render epigenetic profile sensitive to external environmental influence - Novakovic et al, 2013
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17
Q

What is the influence postnatal maternal care?

A
  • epigenetic programming by maternal behaviour
  • low licking and grooming → stuff → decreased GR expression → high corticosterone levels, high anxiety, low licking or grooming
  • high licking and grooming → increased GR expression → low corticosterone levels, low anxiety, high licking
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18
Q

What are components of diet that can contribute a methyl group to DNA?

A
  • folate
  • vitamin B2
  • vitamin B6
  • vitamin B12
  • choline
  • all one carbon donors → SAM-e → primary methyl donor in all eukaryotes → addition of a methyl group
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19
Q

What is the effect of maternal diet on the neonatal epigenome?

A
  • a focus on folate
  • maternal epigenetics and methyl supplements affect agouti gene expression in A/a mice
20
Q

What are other environmental epigenetic regulators as seen in animal studies?

A
  • maternal care and stress
  • endocrine disruptors
  • folate and micronutrients
  • assisted reproduction
    • superovulation and/or embryo culturing
  • alcohol exposure
  • smoking
  • pollution/heavy metals/particulates
  • many others emerging
21
Q

What is seen in a methylation analysis of twins?

A
  • classical twin model
    • monozygotic (MZ) twins share 100% of genetic material
    • dizygotic (DZ) twins share ~50% of genetic variation
    • MZ correlation greater DZ correlation (genetic influence)
    • within pair MZ differences (environmental/stochastic influence)
  • discordant monozygotic twins
    • insights into non-genetic mechanisms in disease
22
Q

What is the PETS timeline?

A
  • 18-20 weeks - recruitment, diet, stress, lifestyle, conception questionnaires
  • 28 weeks
    • maternal questionnaires (as above if needed)
    • maternal blood → serum/plasma storage
  • birth - baby measurements, birth data, (questionnaire data)
    • cord blood → serum/plasma (-70C), WBC/CBMC (LN2)
    • placenta → multiple biopsies in RNA later (-70C)
    • cord tissue → biopsy (-70C), HUVECs (LN2)
    • buccal swabs → DNA (-70C)
  • 18mth followup
    • questionnaires (diet, lifestyle, general), baby measurements
    • peripheral blood → serum/plasma (-70C)
    • buccal swabs → DNA (-70C)
  • PETS = the peri/post-natal epigenetic twins study
23
Q

What is genome-wide methylation data?

A
  • evidence of environmental effects
  • clear evidence of variabilty within MZ twins
24
Q

What is the relationship between smoking and epigenetics?

A
  • maternal
  • DNA methylation of 1,062 newborn cord bloods from the Norwegian Mother and Child Cohort Study (MoBa)
  • replication in newborn epigenetic study - NEST
25
Q

What is replication of methylation at 26 CpG sites?

A
26
Q

What are outstanding questions?

A
  • how reproducible are the data in other cohorts?
  • what is the size of any ‘regional’ effect?
  • is there any tissue specificity?
  • dosage and timing effects?
  • functional relevance? is there an effect on expression?
  • is there any evidence for stability postnatally – (epigenetic ‘legacy’) in the absence of continued exposure?
  • do genetic factors contribute to inter-individual methylation variation?
27
Q

What is the regional effect of maternal smoking AHRR intron 1 methylation in CBMCs?

A
28
Q

Is there a difference between those who smoked early and those who smoked throughout pregnancy?

A
  • yes - prolonged exposure is necessary
29
Q

What is the difference between buccal epithelial and placent of smoking vs non-smoking mothers?

A
30
Q

What is the difference in mean methylation between never smokers and smokers at birth and 18m?

A
31
Q

What role does genetics play in regulating the early life epigenetic profile?

A
  • CBMCs
    • 11/16 MZ cluster - 69%
    • 5/10 DZ cluster - 50%
  • HUVECs
    • 6/13 MZ cluster - 46%
    • 0/8 DZ cluster - 0%
  • placenta
    • 7/8 MZ cluster - 88%
    • 3/6 DZ cluster - 50%
  • contribution of genetic variation to transgenerational inheritance of DNA methylation
  • the effect of geneotype and in utero environment on interindividual variation in neonate DNA methylomes
  • GeMes, Clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease
32
Q

Summary thus far

A
  • variation in DNA methylation in MZ twins at birth highlights the importance of environment in specifying neonatal epigenetic profile
  • clear evidence now exists confirming a genetic contribution to the human epigenetic profile
  • known carcinogens (e.g. smoking) can induce stable epigenetic change even in utero
33
Q

What is evidence for epigenetic disruption in complex phenotypes/disease in humans?

A
  • uniequivocal evidence for:
    • imprinting disorders (BWS, SRS)
    • ICF syndrome
    • all adult cancers
  • evidence emerging for:
    • immune related (T1D, MS, atopy, asthma, arthritis)
    • neurological (bipolar, schiz, MD< eating disorders, Alzheimers, Parkinsons)
    • musculoskeletal (osteoporosis)
    • metabolic (type II diabetes, obesity)
    • cardiovascular (foetal programming)
34
Q

What is epigenetic disruption in complex human disease?

A
  • personalised epigenomic signatures that are stable over time and cobary
  • genome wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood
35
Q

Is there replication of T2D findings?

A
  • genome-wide DNA methylation analysis of human pancreatic islets from Type 2 Diabetic and Non-Diabetic donors identifies candidate genes that influence insulin secretion
  • epigenome-wide association study reveals longitudinally stable DNA methylation differences in CD4+ T cells from children with IgE-mediated food allergy
  • genome-scale case control analysis of CD4+ T cell DNA methylation in juvenile idiopathic arthritis reveals potential targets involved in disease
36
Q

What kind of disease is cancer?

A
  • epigenetic
  • CpG island methylation → methylation spreading
  • tumour suppressor gene expression potential → gene silencing
  • widespread hypomethylation (for example at late-replicating LADs)
    • mislocalisation of DNMT1
37
Q

What is utilising archived clinical material for DNA methylation analysis?

A
  • bone marrow is taken for patient diagnosis
  • excess bone marrow is archived
  • suitable for methylation analysis (Wong, 2008)
  • retrospective cohort of more than 600 patients with clinically annotated samples, including outcome
38
Q

What defines paediatric pre-B cell acute lymphoblastic leukaemia?

A
  • a distinct DNA methylation signature
  • genome wide analysis of 17 matched pairs of ETV6-RUNX1 subtype paediatric ALL cases (infinium 27k methylation microarray - targeting gene promoters)
  • heatmap shows 115 probes with leukaemic specific methylation
  • associated with genes previously implicated in leukaemia, other malignancies and haematopoietic development
  • A 15 gene signature accurately defines ALL
    • validated on a subset of 85 mixed ALL patients
  • represents a pan-ALL biomarkers
  • the diagnostic potential of a subset of the markers was investigated
39
Q

What is DNA methylation as a biomarker for disease?

A
  • watch this
40
Q

What is epigenetic deregulation in paediatric acute lymphoblastic leukaemia?

A
  • watch this
41
Q

What are prognostic signatures in paediatric pre B-cell ALL?

A
  • LAT1 intra-genic DNA methylation is associated with relapsed paediatric ALL
42
Q

What is other recent cancer research?

A
  • stability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigating molecular mechanisms of drug resistance
  • integrated genomic analysis of relapsed childhood acute lymphoblastic leukaemia reveals therapeutic strategies
  • hypermethylation and down-regulation of DLEY2 in paediatric acute myeloid leukaemia independent of embedded tumour suppressor miR-15a-16-1
  • optimised DNA extraction for methylome profiling using neonatal dried blood
43
Q

summary 3

A
  • mounting evidence links distinct epigenetic change to complex phenotypes in humans
  • in some instances evidence of epigenetic change exists prior to phenotypic onset
  • all human cancers show a disrupted epigenetic profile
  • epigenetic profiling has utility at multiple levels in paediatric cancers
    • diagnosis, disease monitoring, prognostication
44
Q

What are caveats?

A
  • general lack of reproduction
    • differences in phenotyping
    • different analytical approaches
  • generally insufficient sample size
    • technological and $$$ limitations
  • general lack of assessment in appropriate target tissue
  • lack of longitudinal analysis - cause vs effect?
  • efect sizes are often questionable
45
Q

What is the relationship between methylation and alzheimer’s?

A
  • methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer’s disease
  • Alzheimer’s disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci
46
Q

What is the prevailing model?

A
  • epigenetic variation, disease and ageing
  • determined by:
    • genetic variation
    • environment/lifestyle (including diet)
    • stochastic factors
    • telomere length
    • other?
47
Q

What are conclusions?

A
  • epigenetic variation defines who we are
  • mounting evidence links environmentally induced epigenetic change in utero to altered phenotype in animal models
  • the in utero period is critical in determining the overall epigenome in humans
  • the early life epigenome is highly dynamic and sensitive to environmental influence
  • also regulated by underlying genetic effects in a tissue specific manner
  • preliminary data link altered DNA methylation to complex diseases such as allergy and cancer in children AND to specific exposures in utero

BIOL30001 (35 decks)

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