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.
2013 03 12_epigenetic_profiling
Slides availablewww.bioinformatics.be 12 Maart 2013
Lab for Bioinformatics and computational genomics 10 “genome hackers” mostly engineers (statistics) 42 scientists technicians, geneticists, clinicians >100 people hardware engineers,mathematicians, molecular biologists
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)
DNA Methylation Differentiates Totipotent EmbryonicStem Cells from Unipotent Adult Stem Cells Alex Meissner, Henry Stewart Talks
Reprogramming the DNA methylome Paula Vertino, Henry Stewart Talks
Epigenetic Changes areImportant 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
Example of Methylationvs Mutation: Colon & Breast Cancer Dx CDx Methylated Mutated Source: Schuebel et al 2007 76-100 51-75 21-50 1-20
MGMT BiologyO6 Methyl-GuanineMethyl TransferaseEssential DNA Repair EnzymeRemoves alkyl groups from damaged guaninebasesHealthy individual: - MGMT is an essential DNA repair enzyme Loss of MGMT activity makes individuals susceptible to DNA damage and prone to tumor developmentGlioblastoma patient on alkylator chemotherapy: - Patients with MGMT promoter methylation show have longer PFS and OS with the use of alkylating agents as chemotherapy
MGMT PromoterMethylation PredictsBenefit 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
Next_nextmiRNA, (l)ncRNA, CIS/TRANS splicing, SV, fusion loci ,bidirectional promoters ?RNA_seq: sequence RNA molecules Next Gen PlatformTotal RNA_seq: all RNA molecules (normalisation procedure)Directional Total RNA_seq: before amplification use different5’ and 3’ adaptorsIntegrated Directional Total RNA_seq: Combine with otherdatasets eg. enrichment sequencing data, visualise and queryin genome browser 32
GCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT 25% 50% 25%GCATCGTGACTAGCGACTGATCGATGGATGCTAGCATGCATCGTGACTAGCGACTGATCGATGGATGCTAGCAT Dense methylated needed for transcriptional silencing Are there alleles with all three positions methylated ?
Deep Sequencing unmethylated alleles methylated alleles less methylation more methylationGCATCGTGACTTACGACTGATCGATGGATGCTAGCAT
ConclusionCombination of different sequencingtechniques is emerging as best practiceBioinformatics is challengingMethods for normalisation underconstructionReference databases are generatedData visualization and integration is key 41
Slides availablewww.bioinformatics.be 4th December 2012 Johns Hopkins Bloomberg School of Public Health