7. Defining Epigenetics
Genome
DNA Reversible changes in gene
expression/function
Without changes in DNA
Chromatin sequence
Epigenome Can be inherited from
precursor cells
Gene Expression Allows to integrate intrinsic
with environmental signals
Phenotype
(including diet)
8. DNA Methylation Differentiates Totipotent Embryonic
Stem Cells from Unipotent Adult Stem Cells
Alex Meissner, Henry Stewart Talks
15. Epigenetic Changes are
Important in Causing Cancer
GENETIC EPIGENETIC
Example: Example:
Replication errors Chromatin modification errors
X X
Altered Altered
DNA sequence chromatin structure
Oncogenesis
Altered Altered levels of
DNA/mRNA/proteins mRNA/proteins
Tumor
16. Example of Methylation
vs Mutation: Colon & Breast Cancer
Dx
CDx
Methylated Mutated
Source: Schuebel et al 2007
76-100 51-75 21-50 1-20
17. MGMT Biology
O6 Methyl-Guanine
Methyl Transferase
Essential DNA Repair Enzyme
Removes alkyl groups from damaged guanine
bases
Healthy individual:
- MGMT is an essential DNA repair enzyme
Loss of MGMT activity makes individuals susceptible
to DNA damage and prone to tumor development
Glioblastoma patient on alkylator chemotherapy:
- Patients with MGMT promoter methylation show
have longer PFS and OS with the use of alkylating
agents as chemotherapy
18. MGMT Promoter
Methylation Predicts
Benefit form DNA-Alkylating Chemotherapy
Post-hoc subgroup analysis of Temozolomide Clinical trial with primary glioblastoma
patients show benefit for patients with MGMT promoter methylation
Median Overall Survival
21.7 months
plus
temozolomide
12.7 months
radiotherapy
radiotherapy
Adapted from Hegi et al.
NEJM 2005
352(10):1036-8.
Non-Methylated Methylated Study with 207 patients
MGMT Gene MGMT Gene
32. Next_next
miRNA, (l)ncRNA, CIS/TRANS splicing, SV, fusion loci ,
bidirectional promoters ?
RNA_seq: sequence RNA molecules Next Gen Platform
Total RNA_seq: all RNA molecules (normalisation procedure)
Directional Total RNA_seq: before amplification use different
5’ and 3’ adaptors
Integrated Directional Total RNA_seq: Combine with other
datasets eg. enrichment sequencing data, visualise and query
in genome browser
32
38. GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
25% 50% 25%
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT
Dense methylated needed for transcriptional silencing
Are there alleles with all three positions methylated ?
39. Deep Sequencing
unmethylated alleles
methylated alleles less methylation
more methylation
GCATCGTGACTTACGACTGATCGATGGATGCTAGCAT
41. Conclusion
Combination of different sequencing
techniques is emerging as best practice
Bioinformatics is challenging
Methods for normalisation under
construction
Reference databases are generated
Data visualization and integration is key
41
Here, we define epigenetics and depict the relationship between the genome and the epigenome The genome is hereditary information encoded in the DNA and the epigenome is the way cells express the encoded information 1 The epigenome is a ‘bridge’ between genotype and phenotype (epigenetics governs genotype and phenotype) Epigenetic information is included in the genome of a cell but is not encoded by the DNA 1,2 Epigenetic information may be inherited from precursor cells 1 Epigenetic changes affect chromosome structure to alter gene expression 1,2 References Goldberg AD et al. Cell 2007;128:635–8. Bernstein BE et al. Cell 2007;128:669–81.
There is growing evidence that epigenetic modifications are also crucial to the onset and progression of cancer 1 On the right of the slide, we see that changes in gene expression due to chromatin modifications (e.g. histone acetylation, DNA methylation) lead to altered levels of mRNA and proteins Altered levels of proteins involved in cell growth and death can lead to deregulated cell proliferation and survival, resulting in cancer 2 Examples: Silencing of p15 tumor suppressor gene expression 3 Aberrant expression of IGF2 4 Silencing of ER- α gene expression 3 References Bolden JE et al. Nat Rev Drug Discov 2006;5:769–84. Miranda E et al. Br J Cancer 2006;95:1101–7. Esteller M. N Engl J Med 2008;358:1148 – 59. Feinberg AP. Nature 2007;447:433–40.