The epigenetic regulation of DNA-templated processes has been intensely studied over the last 15 years. DNA methylation, histone modification, nucleosome remodeling, and RNA-mediated targeting regulate many biological processes that are fundamental to the genesis of cancer. Here, we present the basic principles behind these epigenetic pathways and highlight the evidence suggesting that their misregulation can culminate in cancer. This information, along with the promising clinical and preclinical results seen with epigenetic drugs against chromatin regulators, signifies that it is time to embrace the central role of epigenetics in cancer.

1. Under supervision
of
Professor

2. CAUSE VS. CONSEQUENCE OF CANCER FOR EPIGENETIC
ABNORMALITIES
2
epigenetics genetics
Diagnosis
Prognosis
Targeted for therapy

3. DNA METHYLATION
 The methyl group of 5mC lies in the major groove
of the double helix and can interfere with
transcription factor binding to prevent gene
expression.
 Cytosine pairs with guanine by means of a
phosphate group, and this dinucleotide (CpG) has
been a major focus of epigenetic research because
of its capacity to directly silence gene expression,
particularly with respect to tumor-suppressor genes
in carcinogenesis. CpG sites are unevenly distributed
throughout the genome, concentrating in repetitive
sequences such as tandem and interspersed
repeats, distal gene regulatory regions, and CpG
islands
BIRD A. 2002. DNA METHYLATION PATTERNS AND EPIGENETIC MEMORY. GENES DEV 16:6-21

4. 4
M
CGGGCATCA
MECP2 and the MBD family of proteins, which bind to
methylated cytosines and repress gene transcription by
blocking transcription factors.
ILLINGWORTH R S, BIRD AP. 2009. CPG ISLANDS—“A ROUGH GUIDE.” FEBS LETT 583:1713-1720

5. DNA METHYLATION
5
5`AAAGATCCGGCGTA3`
CH 3
CCGGCGTA3
CH3
Feinberg and Vogelstein
1983

6. REPETITIVE ELEMENTS
6
Repetitive elements make up about half of the genome
and are normally heavily methylated.
 Centromeric tandem repeats
 adjacent-centromeric (juxta-centromeric) tandem
repeats
 Alu and LINE
are the most frequently studied
repetitive elements in cancer
that are found to be
hypomethylated.
EHRLICH M. 2009. DNA HYPOMETHYLATION IN CANCER CELLS. EPIGENOMICS 1:239-259.
Hypomethylation of LINE-1 elements occurs in
colorectal cancer

7. REPETITIVE ELEMENTS
7
• Play key role in keeping the DNA
packaged into heterochromatin
at the point of sister chromatid
association
• Chromosome stability
Hypomethylation of these regions can lead to
chromatin decondensation and chromosome
rearrangements through unstable translocations, leading to
widespread genomic instability Additionally, loss of
heterochromatin can affect the copy number of genes
involved in tumorigenesis.

8. DNA METHYLTRANSFERASES
8
M
M M M M M
DNMT overexpression
DNMT1, DNMT3a, and DNMT3b are known to contribute to
the global pattern of cytosine methylation
KULIS AND ESTELLER 2010; OKANO ET AL. 1999

9. DNA METHYLTRANSFERASES
DNMT1
 methylation of CpG sites in newly synthesized daughter DNA strands to match the methylation pattern
of the parental strand
 directly binds histone deacetylases to promote heterochromatin formation and silence gene activity
DNMT3
DNMT3a and DNMT3b are classified as de novo enzymes that are essential for establishment of mammalian
development methylation patterns during embryogenesis and germ-cell development
9
BIRD 2002; KULIS AND ESTELLER 2010; LI ET AL. 1992
KULIS AND ESTELLER 2010

10. DNA METHYLTRANSFERASES
10
DNMT gene
Overexpression in tumor cells
DNMT overexpression seems to be a common
characteristic of tumors, although only DNMT1 and
DNMT3a/b are implicated in tumorigenesis
It has been proposed that these enzymes cooperate to initiate and maintain de novo methylation in cancer cells
(Rhee et al. 2002). DNMT1 and DNMT3b have been shown to form a complex with oncogenic transcription
factors to induce de novo methylation of CpG islands in promoter regions (Di Croce et al. 2002). Patients with
DNMT3a mutations had significantly worse prognosis in acute myeloid leukemia (Ley et al. 2010). Therefore,
DNMTs in cancer have a crucial role in the hypermethylation that is found on CpG islands and its subsequent
downstream effects.

11. CPG ISLANDS AND GENE EXPRESSION
 CpG islands occupy approximately 60% of human gene promoters, most of which are constitutively
expressed genes [1]
 The normal hypomethylated pattern of CpG islands is found to be consistent across various types of
somatic tissues despite tissue-specific differences, illustrating that DNA methylation of these islands is
not used as a regulatory mechanism of gene expression[2]
 The cancer cell genome is characterized by hypermethylation of CpG islands in promoter regions
11
[1] Vu TH, Li T, Nguyen D, Nguyen BT, Yao XM, Hu JF, Hoffman AR. 2000. Symmetric and asymmetric DNA methylation in the human IGF2-H19 imprinted
region. Genomics 64:132-143.
[2] Cotton AM, Lam L, Affl eck JG, Wilson IM, Penaherrera MS, McFadden DE, Kobor MS, Lam WL, Robinson WP, Brown CJ. 2011. Chromosomewide DNA
methylation analysis predicts human tissue-specifi c X inactivation. Hum Genet 130: 187-201.
M M M M MM
CpG island
Promoter region
CpG island

12. CPG ISLANDS AND GENE EXPRESSION
12
 In contrast with hypomethylation of
intergenic CpG sites in cancer that
lead to genomic instability,
hypermethylation of CpG islands
promotes the progression of
tumorigenesis by silencing tumor-
suppressor genes.

13. CPG ISLANDS AND GENE EXPRESSION
13
APC involved in cell-cycle regulation,
cell–cell adhesion, and cell mobility
inactivated by
hypermethylation in
many lung, breast,
and colorectal
cancers [3]
hypermethylated in
brain and thyroid
cancers[2]
Prevents rapid proliferationPTEN
Suppression of p16, a cell-cycle
regulator, occurs in essentially all common human
cancers[1]
[1] LIGGETT WH, SIDRANSKY D. 1998. ROLE OF THE P16 TUMOR SUPPRESSOR GENE IN CANCER. J CLIN ONCOL 16:1197-1206.
[2] FAN S, ZHANG X. 2009. CPG ISLAND METHYLATION PATTERN IN DIFFERENT HUMAN
[3] ILLINGWORTH R S, BIRD AP. 2009. CPG ISLANDS—“A ROUGH GUIDE.” FEBS LETT 583:1713-1720.

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15. CpG Island Hypermethylation--- Single Biomarker
 Biomarker
 Distinguish cancer from normal cells in the
sample
o e.g. tumour vs benign skin, tumour vs
normal prostate
o e.g. cells or tumour DNA found as cell-free
DNA in the blood, from normal blood
 Identify a specific feature of the cancer
 DNA hypermethylation biomarkers are
favored, as detection is more sensitive
15

16. CHROMATIN REMODELING IN CANCER
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17. CHROMATIN REMODELING IN CANCER
 Chromatin conformation is controlled by
chemical modifications, mainly covalent
modifications, of the N-terminus tails of the
histone proteins that form the core of the
nucleosome. Histone modifications can affect
the interaction between histone proteins and
DNA as well as between adjacent histone
proteins. Histone modification is a dynamic
process, with enzymes catalyzing the addition
of covalent modifications (“writers”), their
removal (“erasers”), and recognition of marks
previously laid down (“readers”) (Wang et al.
2007). Dysregulation of each of these classes
of enzymes has been associated with a variety
of cancer types.
17

18. CHROMATIN REMODELING IN CANCER
 methylation at specific histone tail residues is
associated with both transcriptional activation
and repression
 Histone methylation occurs at both arginine and
lysine residues on the tails of histone proteins
H3 and H4
 Lysine methylation is catalyzed by histone-
lysineN-methyltransferases, also known as K-
methyltransferases, and involves the transfer of
methyl groups from the cofactor S-adenosyl
methionine
Histone Acetylation
 histone acetylation is strongly associated with
transcriptional activation
 Histone acetylation occurs on lysine residues
and is thought to enhance transcription by
charge neutralization of the positively charged
histones
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Histone Methylation

19. 19
JMJD2C
JMJD2C is a K-demethylase that
catalyzes removal of methylation
marks from H3K9, a mark typically
associated with gene repression
K9
EZH2(enhancer of zest2)
In many cancers EZH2 is overexpressed both
at the transcriptional and protein levels. EZH2
overexpression has been described as
important in prostate cancer, where an
increase in EZH2 protein staining in the cell
nucleus was observed with a progression
from benign to metastatic disease
MLL(mixed lineage leukemia
The mixed lineage leukemia (MLL) is a
K-methyltransferase that catalyzes the
methylation of H3K4. MLL acts in
opposition to polycomb repressive
complex proteins, activating genes
involved in development and
differentiation

20. 20
MOLECULAR BIOLOGY OF THE CELL, ALBERTS 2015

21. CANCER TYPES
 Skin cancer
Melanoma is a deadly skin cancer that originates from melanocytes. Several epigenetic alterations are
known to play a role in the transition of melanocytes to melanoma cells. These alterations are the
consequence of deregulation of their corresponding enzymes. Several histone methyltransferases and
demethylases are among these enzymes.
 Prostate cancer
Alterations in histone acetylation and DNA methylation occur in various genes influencing prostate cancer.
More than 90% of prostate cancers show gene silencing by CpG island hypermethylation of the GSTP1 gene
promoter, which protects prostate cells from genomic damage that is caused by different oxidants or
carcinogens.
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22. CANCER TYPES
 Leukemia
Recent studies have shown that the mixed-lineage leukemia (MLL) gene causes leukemia by rearranging
and fusing with other genes in different chromosomes, which is a process under epigenetic control
 Sarcoma
Several oncogenes and tumor suppressor genes are epigenetically altered in sarcomas. These include APC,
CDKN1A, CDKN2A, CDKN2B, Ezrin, FGFR1, GADD45A, MGMT, STK3, STK4, PTEN, RASSF1A, WIF1, as well as
several miRNAs. Expression of epigenetic modifiers such as that of the BMI1 component of the PRC1
complex is deregulated in chondrosarcoma, Ewing's sarcoma, and osteosarcoma, and expression of the
EZH2 component of the PRC2 complex is altered in Ewing's sarcoma and rhabdomyosarcoma. Similarly,
expression of another epigenetic modifier, the LSD1 histone demethylase, is increased in chondrosarcoma,
Ewing's sarcoma, osteosarcoma, and rhabdomyosarcoma.
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