Lecture 04 - Dept. of Physiology and Biophysics, Weill Cornell
Clinical and Research Genomics Epigenomes, DNA Modifications, and Chromatin Dynamics • Aberrant DNA methylation and Cancer: (Li) • DNA modifications and their detection, Pacbio, RRBS, MeDIP, mC, hmC (Zhu) • Chromatin changes and methods: ChIP-Seq, HiC, CCC (Elemento) Aberrant DNA Methylation in Cancer Sheng Li, PhD Instructor of Bioinforma<cs Department of Neurological Surgery Weill Cornell Medical College Aberrant DNA methylation in cancer • DNA methylation dynamics • DNA methylation is hallmark of cancer • DNA methylation sequencing and public resources of epigenetic data hBp://www.ks.uiuc.edu/ Aberrant DNA methylation in cancer • DNA methylation dynamics • DNA methylation is hallmark of cancer • DNA methylation sequencing and public resources of epigenetic data hBp://www.ks.uiuc.edu/ Epigenetic codes DNA: gene<c code (ATCG) Epigene<c code: • Can be inherited. • Can be transmiBed by mother to daughter cells. • Is important to cellular process and regula<on. • Has plas<city. www.promega.com/ Genomic distribution of methylated cytosine in a typical vertebrate genome CpG islands (CGIs), which oSen overlap with promoter regions, generally remain unmethylated, whereas CG-‐ poor promoters are methylated when not ac<ve. Schubeler, Nature, 2015 CTCF occupancy linked to DNA methylation plasticity • 11-‐zinc finger protein • Transcrip<onal repressor • Regula<ng the structure chroma<n Wang, Genome research, 2012 CTCF occupancy linked to DNA methylation plasticity • 11-‐zinc finger protein • Transcrip<onal repressor • Regula<ng the structure chroma<n Wang, Genome research, 2012 CTCF occupancy linked to DNA methylation plasticity • 11-‐zinc finger protein • Transcrip<onal repressor • Regula<ng the structure chroma<n Wang, Genome research, 2012 Writers and erasers in DNA methylation IDH1/2 Schubeler, Nature, 2015 Li, 2013 Writers and erasers in DNA methylation IDH1/2 Schubeler, Nature, 2015 Li, 2013 Aberrant DNA methylation in cancer • DNA methylation dynamics • DNA methylation is hallmark of cancer • DNA methylation sequencing and public resources of epigenetic data Methylation changes are a hallmark of cancer Nephew and Huang, 2003 Aberrant DNA methylation in cancer • DNA methylation levels • Epigenetic heterogeneity DNA methylation fingerprint is very different in each cancer excluding CpG sites with <ssue-‐specific methyla<on Fernandez et al, Genome Research, 2012 DNA methylation fingerprint is very different in each cancer Fernandez et al, Genome Research, 2012 Single somatic mutation causes focal hypomethylation in leukemia Focal Hypomethyla<on Phenotype Associated with DNMT3A R882 Muta<ons Russler-‐Germain DA, Cancer Cell, 2014 DNA methylation profiling as a diagnostic tool Glioblastoma: CIMP+ group have beBer clinical outcome CpG island methylator phenotype (CIMP) that defines a distinct subgroup of glioblastoma Noushmehr, Cancer cell, 2010 Ependymoma: CIMP+ renders worse clinical outcome Transcriptome defined group A and B WiB, Cancer cell, 2011 Group A with worse clinical outcome is CIMP+ Mack, Nature, 2014 DNA methylation contributes to heterogeneity in cancer Increased methylation variance of common CpGs sites across human cancer types Using the CpGs that showed the largest increase in variability, performed hierarchical clustering on the normal samples. Hansen 2011 High variability regions of gene expression associated with blocks Hansen 2011 Intra-tumor epigenetic heterogeneity measured by locally disordered reads CLLs consistently displayed higher intrasample variability of DNA methyla<on paBerns across the genome, which appears to arise from stochas<cally disordered methyla<on in malignant cells Landau, Cancer cell, 2014 Transcriptome heterogeneity is associated with promoter methylation heterogeneity Landau, Cancer cell, 2014 Locally Disordered Methylation Is Associated with Adverse Clinical Outcome Landau, Cancer cell, 2014 Aberrant DNA methylation in cancer • DNA methylation dynamics • DNA methylation is hallmark of cancer • DNA methylation sequencing and public resources of epigenetic data Various approaches for DNA methylation quantification DNA methylation quantification Single base resolution Whole Genome Bisulfite Sequencing(WGBS) Reduced Representaation bisulfite sequening (RRBS) Roche non single base resolution Infinium 450K BeadChip MethylCapture Agilent HELP array Antibody based sequencing MeDIPSeq MethylCap Single base resolution methylated cytosine sequencing approaches hBp://support.illumina.com/ Single base resolution methylated cytosine sequencing approaches Extracted DNA Whole genome hBp://support.illumina.com/ Enriched for high CpG density regions including CpG island/shores Enriched assay WGBS RRBS Methyl-capture seq 27 M CpGs $5000/ sample 3 M CpGs $800/ sample 3-5 M CpGs $1800/ sample eRRBS (Enhanced Reduced Representation Bisulfite Sequencing) RRBS MspI diges<on Less star<ng material 1000ng -‐>5ng eRRBS Size selec<on (40-‐220 bp) Size selec<on (70-‐320 bp) bisulfate treatment PCR and sequence Akalin, GarreB-‐Bakelman, 2012 Public resources hBp://cancergenome.nih.gov Epigenome roadmap Tissues and cell types profiled in the Roadmap Epigenomics Consortium Kundaje, Nature, 2015 Comprehensive epigenetic profiling Kundaje, Nature, 2015 hBp://egg2.wustl.edu/roadmap/ web_portal/ Kundaje, Nature, 2015 Summary • DNA methylation dynamics • DNA methylation is hallmark of cancer • DNA methylation sequencing and public resources of epigenetic data Questions?
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