1. Epigenetics and Cancer
Jordina Casanova Vilar
Genomics

2. Introduction Epigenetics
Conrad Waddington: “Heritable changes in a cellular
phenotype independent of alterations in the DNA sequence”
Epigenetics
DNA-based processes:
Transcription
DNA Repair
Replication
DNA methylation
Nucleosome remodeling
Histone modification
RNA-mediated targeting
Nebbioso A, Tambaro FP, Dell'AversanaC, Altucci L (2018) Cancer epigenetics: Moving forward. PLoS Genet 14(6): e

3. Introduction Development of global proteomic and genomic technologies
Appreciation of epigenetic complexity and plasticity
NGS
Maps of nucleosome positioning
ChIP-Seq
Chromatin conformation
TF binding sites
Localization of histone and DNA modifications
Catalog of recurrent somatic mutations in epigenetic regulators
Whole-genome sequencing
Identification of driver mutations implicated in oncogenesis

4. Epigenetic Pathways Connected to Cancer

5. 1. DNA Methylation CpG islands  70% of mammalian promoters
Hypermetilation of CpG islands of tumor-supressor genes
Associated with reduced expression
Important in transcriptional regulation
5-10% CpG islands become abnormally methylated in cancer genomes
Altered during malignant transformation
Nebbioso A, Tambaro FP, Dell'AversanaC, Altucci L (2018) Cancer epigenetics: Moving forward. PLoS Genet 14(6): e

6. Maintenance methyltransferase De novo methyltransferases
1. DNA Methylation
DNMT3A
Maintenance methyltransferase
DNMT1
De novo methyltransferases
DNMT3B
Replication
Embryogenesis
Sequencing of cancer genomes:
Recurrent mutations in DNMT3A in up to 25% of patients with acute myeloid leukemia (AML). Impact in prognosis.
Ley, T.J., Ding, L., Walter, M.J., McLellan, M.D., Lamprecht, T., Larson, D.E., Kandoth, C., Payton, J.E., Baty, J., Welch, J., et al. (2010). DNMT3A mutations in acute myeloid leukemia. N. Engl. J. Med. 363, 2424–2433.

7. 1. DNA Methylation TET proteins
Convert 5mC to 5hmC in an Fe(II) and α-ketoglutarate-dependent manner
Mutations in IDH1 and IDH2  70% of patients with secondary glioblastoma mutiforme and myeloid malignancies, most notably AML.
Reduction of α-KG to 2-hydroxyglutarate
Loss of function of TET2
Increase in DNA methylation levels
Cimmino, L., Abdel-Wahab, O., Levine, R. and Aifantis, I. (2011). TET Family Proteins and Their Role in Stem Cell Differentiation and Transformation. Cell Stem Cell, 9(3), pp

8. 2. Histone Modifications KATs: Lysine Acetyltransferases
Histone Acetylation
Histone Deacetylation
HDACs
Neutralizes lysine’s + charge  weaken electrostatic interaction between histones and DNA
Chimeric fusion proteins seen in leukemia recruit HDACs  gene silencing
“Open” chromatin conformation
Relaxed structure
Greater levels of gene transcription
Mutation of HDAC2 in sporadic tumors with microsatellite instability and tumors in non-polyposis colorectal carcinoma
HDAC2 involved in gene repression mediated by Rb
Loss of function
 hyperacetilation
 reexpression of genes regulated by Rb
KATs: Lysine Acetyltransferases
Implicated in neoplasic transformation
Viral oncoproteins associate with them
Chromosomal translocations (MLL-CBP, MOZ-TIF2)
Coding mutations (solid and hematological malignances)
Ropero, S. and Esteller, M. (2007). The role of histone deacetylases (HDACs) in human cancer. Molecular Oncology, 1(1), pp

9. 2. Histone Modifications
Histone Methylation
Arginine
Lysine
Histidine
Cancer genomes:
Translocations/mutations in KMT (MMSET, EZH2, MLL)
PRC2
- Methylation of histone H3 (chromatin compactor)
EZH2 as catalytic component
Margueron, R. and Reinberg, D. (2011). The Polycomb complex PRC2 and its mark in life. Nature, 469(7330), pp
Overexpression of EZH2  poor prognosis in prostate and breast cancer
Coding mutations in EZH2 in lymphoid and myeloid neoplasms

10. 2. Histone Modifications
Histone Phosphorylation
Mitosis, apoptosis, DNA repair, replication, transcription
Serine
Threonine
Tyrosine
Frequently amplified/mutated in hematological malignancies
TK JAK2
Activates expression of hematopoietic oncogenes (Lm2o, MYC)
Phosphorylates H3Y41  disrupts chromatin repressor HP1a binding
Dawson, M.A., Bannister, A.J., Go¨ ttgens, B., Foster, S.D., Bartke, T., Green, A.R., and Kouzarides, T. (2009). JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin. Nature 461, 819–822.

11. 3. Non-coding RNAs
Increasingly recognized to be vital for normal development and compromised in diseases such as cancer
lncRNAs  critical function at chromatin: chaperones or scaffolds for chromatin regulators
HOTAIR
Manipulation of HOTAIR levels within malignant cells can alter the invasive potential
Molecular scaffold for PRC2 complex (chromatin compactor)
Aberrantly overexpressed in advanced breast and colorectal cancer
Kogo, R., et al. (2011). Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 71,6320–6326.
Wang, K.C., and Chang, H.Y. (2011). Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904–914.

12. Epigenetic pathways missregulation can culminate in cancer
Conclusions
DNA methylation, histone modification, and RNA-mediated targeting regulate many biological processes that are relevant for the genesis of cancer
Epigenetic pathways missregulation can culminate in cancer
Appreciation of epigenetic complexity and plasticity has increased over the last few years following the development of several global proteomic and genomic technologies
Identification of driver mutations provide potential targets for therapeutic intervention

13. Bibliography
Cimmino, L., Abdel-Wahab, O., Levine, R. and Aifantis, I. (2011). TET Family Proteins and Their Role in Stem Cell Differentiation and Transformation. Cell Stem Cell, 9(3), pp
Dawson, M. and Kouzarides, T. (2012). Cancer Epigenetics: From Mechanism to Therapy. Cell, 150(1), pp
Dawson, M.A., Bannister, A.J., Go¨ ttgens, B., Foster, S.D., Bartke, T., Green, A.R., and Kouzarides, T. (2009). JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin. Nature 461, 819–822.
Kogo, R., et al. (2011). Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 71,6320–6326
Ley, T.J., Ding, L., Walter, M.J., McLellan, M.D., Lamprecht, T., Larson, D.E., Kandoth, C., Payton, J.E., Baty, J., Welch, J., et al. (2010). DNMT3A mutations in acute myeloid leukemia. N. Engl. J. Med. 363, 2424–2433.
Margueron, R. and Reinberg, D. (2011). The Polycomb complex PRC2 and its mark in life. Nature, 469(7330), pp
Nebbioso A, Tambaro FP, Dell'AversanaC, Altucci L (2018) Cancer epigenetics: Moving forward. PLoS Genet 14(6): e
Ropero, S. and Esteller, M. (2007). The role of histone deacetylases (HDACs) in human cancer. Molecular Oncology, 1(1), pp
Wang, K.C., and Chang, H.Y. (2011). Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904–914.