This document discusses epigenetics and epigenetic modifications. It begins by defining the epigenome and how it can change without altering DNA sequence. The main epigenetic modifications discussed are DNA methylation and various histone modifications such as acetylation, methylation, phosphorylation, ubiquitination, and SUMOylation. These modifications can impact gene expression and transcription. The document then examines how epigenetic abnormalities contribute to various diseases like cancer, diabetes, and neurological disorders. Finally, it reviews some FDA-approved epigenetic therapies that target DNA methyltransferases and histone deacetylases, as well as epigenetic drugs currently in clinical trials.

1. Presented by:
Shaheen Wasil
M.S. Pharm (2nd Sem.)
Pharmacology & Toxicology
National Institute of Pharmaceutical Education & Research (NIPER)
S.A.S. Nagar , Mohali

2. Flow of Presentation
Introduction
Various epigenetic modifications
Epigenetics in disease
Therapeutic targeting of epigenetic modifications
Conclusion

3. Introduction
What is epigenome?
What does the epigenome do?
Is the epigenome inherited?
Can the epigenome change?
What makes the epigenome change?

5. Epigenetic Modifications
DNA Methylation
(A) In an unmethylated state, a transcription factor may bind to a CpG site
and promote gene expression. (B) Alternatively, methylation of the CpG site
may alter the affinity between the transcription factor and the CpG site,
ultimately disrupting gene expression.
Hamm et al , Pharmacology & therapeutics 151 (2015): 72-86.

6. Contd…
 DNA methylation is established and maintained by a family of
enzymes known as DNA methyltransferases(DNMTs)
 DNMT1
Most abundant DNMT
Maintainance of DNA methylation
Greater affinity for hemimethylated DNA
 DNMT3A & DNMT3B
De novo methylases, establish DNA methylation
No preference for hemimethylated or unmethylated DNA
 DNA methylation is removed by DNA demethylases(TET proteins).

7. Histone Modifications
1. Acetylation
2. Methylation
3. Phosphorylation
4. Ubiquitination
5. SUMOylation
 Have important role in transcriptional regulation,
DNA repair, DNA replication, alternative splicing and
chromosome condensation
Portela et al, Nature biotechnology 28.10 (2010): 1057-1068.
Histone Code

8. Acetylation
 Involves acetylation of the lysine residues on the histone tails
mainly of H3 and H4 histones
 Represents active transcription
 Enzymes involved in the acetylation of histones are Histone
Acetyl Transferases (HATs)-GNAT, CBP/P300 etc
 Enzymes involved in removal of these acetylation marks are
Histone Deacetylases- Class I HDAC, Class II HDAC, Class IV
HDAC(zinc dependent metallohydrolases), and Class III HDAC
(NAD+ dependent deacetylases)

9. Methylation
 Involves methylation of the lysine residues in the histone tails
 Depending upon the position of lysine and number of methyl groups, this
mark can represent both active and repressed transcription
me3/me3 at H3K4, H3K36 and H3K79 represent active transcription
H3K9me2/me3, H3K36me2, H4K20me1 and H3K27me3 represent
repressed transcription
 The enzymes involved in methylation are the histone lysine methyl
transferases- Set1, Set7/9, etc
 The enzymes involved in the removal of these methyl groups are histone
lysine demethylases-LSD1, JMJD2A, etc

10. Various Histone modifications
 Acetylation (blue), methylation (red), phosphorylation (yellow) and ubiquitination (green)
Portela et al, Nature biotechnology 28.10 (2010): 1057-1068.

11. Mark Transcriptionally relevant sites Biological Role
Methylated cytosine
(meC)
CpG islands Transcriptional Repression
Acetylated lysine
(Kac)
H3 (9,14,18,56), H4 (5,8,13,16), H2A, H2B Transcriptional Activation
Phosphorylated
serine/threonine
(S/Tph)
H3 (3,10,28), H2A, H2B Transcriptional Activation
Methylated lysine
(Kme)
H3 (4,36,79)
H3 (9,27), H4 (20)
Transcriptional Activation
Transcriptional Repression
Ubiquitylated lysine
(Kub)
H2B (123/120)
H2A (119)
Transcriptional Activation
Transcriptional Repression
Sumoylated lysine
(Ksu)
H2B (6/7), H2A (126) Transcriptional Repression
Role of various Epigenetic modifications

12. Epigenetics in Disease

13. Epigenetic Modifications in Human disease
Epigenetic
Aberration
Enzymes
Responsible
Disease Epigenetic Alteration Comments
DNA methylation DNMTs Cancer Global hypomethylation,
hypermethylation
of some CpG island
promoters
Activation of
oncogenes or
repression of TSGs
Diabetes Hypermethylation of
PPARGC1A promoter
Repressed
PPARGC1A
Histone Acetylation HATs and HDACs Rubinstein-Taybi
syndrome
Hypoacetylation Mutation in gene
encoding
CBP, a known HAT
Diabetes Hyperacetylation at
promoters of
inflammatory genes
Histone
Methylation
HMTs and HDMs Cancer H4K20me3 loss Hypomethylation of
DNA
repetitive sequences
Sotos syndrome Decreased H4K20me3
and H3K36me3
Loss of function of
NSD1, a HMT
Alzheimers
Disease
CpG island
hypermethylation
Transcriptional
repression of NEPKelly et al, Nature biotechnology 28.10 (2010): 1069-1078.

14. FDA Approved Epigenetic Therapies
Compound Mechanism of
action
Indications Company Approved in
Vidaza (5-
Azacytidine)
Nucleoside
DNMT
inhibitor
Myelodysplastic syndromes
and
chronic myelomonocytic
leukemia.
Celgene May 2004
Dacogen
(Decitabine)
Nucleoside
DNMT
inhibitor
Myelodysplastic syndromes EisaiTokyo; sublicensed to
Johnson & Johnson
May 2006
Zolinza
(Vorinostat)
HDAC
inhibitor
Cutaneous T-cell lymphoma Merck Oct. 2006
Istodax
(Romidepsin)
HDAC
inhibitor
Cutaneous T-cell lymphoma
and peripheral T-cell
lymphoma
Celgene Nov. 2009
Beleodaq
(Belinostat)
HDAC
inhibitor
Relapsed or refractory
peripheral T-cell lymphoma
Spectrum Pharmaceuticals July 2014
Farydak
(Panobinostat)
HDAC
inhibitor
Multiple Myeloma Novartis Feb. 2015
Targeting Epigenome for Therapy

15. DRUG MEHCANISM DEVELOPER/SOURCE STAGE OF DEVELOPMENT
Hydralazine
Abexinostat (PCI-24781)
Non-nucleoside DNMT
inhibitor.
PMID: 12632429 Phase
II development as a
chemotherapeutic agent.
Trichostatin A (TSA) Trichostatin A inhibits HDACs
1–9
PMID: 21386836 Side-effects have limited the
clinical
development of TSA.
(−)-epigallocatechin-3-gallate
(EGCG)
CUDC-907
Nucleoside DNMT inhibitor.
Polyphenol isolated from green
tea.
PMID: 16037419 Preclinical.
CP-4200 Nucleoside DNMT inhibitor.
5-Azacytidine derivative
Aqualis (AQUA;
Formerly Clavis Pharma)
Preclinical.
MG98 Non-nucleoside DNMT1
inhibitor.
Antisense oligonucleotide
molecule
designed against DNMT1.
Mirati Therapeutics Inc Phase I studies in adult solid
tumors and AML.
SGI-1027 Non-nucleoside DNMT
inhibitor.
Inhibits DNMT by competing
with
methyl donor
PMID: 19417133 and
23637988
Preclinical
Epigenetic drugs in Clinical and Preclinical development
Histone Deacetylase
Inhibitor (HDACi)
Pharmacyclics
Phase I trials in metastatic solid
tumors and sarcomas
HDAC inhibitor and PI3K
inhibitor
Curis, Inc. Phase I trial in Multiple
myeloma and lymphoma

16. Conclusion
 Epigenetic mechanisms normally regulate various functions like correct
organization of chromatin, genomic imprinting, silencing of repetitive
elements and X-chromosome inactivation
 Epigenetics also is a key player in a variety of human diseases like cancers,
autoimmune diseases, inflammatory diseases and neurologic diseases
 The reversibility of the various epigenetic changes makes these epigenetic
modifications a potential therapeutic target in the treatment of various
diseases like cancers and various DNMT and HDAC inhibitors have been
approved for cancer treatment
 The less well studied modifications in the context of disease like
phosphorylation, ubiquitination and SUMOylation, may expand possibilities
of therapeutic interventions in future

17. Thank You