The document discusses HDAC11, a class IV histone deacetylase enzyme. It provides background on epigenetics and histone acetylation. HDAC11 was discovered in 2001 as a novel HDAC with distinctive features from other classes. It has a gene on chromosome 3 and shares residues with class I and II HDACs. HDAC11 expression is highest in the brain, testis, and other tissues. It is overexpressed in several cancers and may be a potential new target for cancer treatment.

1. Jadavpur University
Project Topic- HDAC11, A New Target For Cancer
Under the Guidance of Prof Dr. Shovanlal Gayen
(Assistant Professor of Dept. of Pharm. Tech, JU)
Department of Pharmaceutical Technology
Name- Swapnamay Halder
Roll No- 001811401047
B. Pharm Fourth Year Second Semester
Department of Pharmaceutical Technology

2. Index
 Introduction to HDAC
 Histone and Nucleosome
 Histone Deacetylase
 Classification of HDAC
 Discovery of HDAC11
 Chemistry of HDAC11
 Sequence of HAC11
 Characteristics of HDAC11
 Expression of HDAC11
 HDAC11 and Tumour
 HDAC Inhibitors
 Conclusion
 Reference

3. Introduction to HDAC11
 In the mid-19th century, following Mendel’s Principle in 1865, the relation between
gene and phenotypic responses were coming to light. In this era, scientist Conrad
Waddington (1905–1975) started a new branch of biogenetics, called Epigenetics.
 Waddington defined Epigenetics as “the branch of biology which studies the causal
interactions between genes and their products, which bring the phenotype into being”.
 Epigenetics is the study of gene and protein expression and their internal relation.
Epigenetics goes into a deep dive into genetic studies, where the expression of a
particular phenotype is altered without any change of sequence in the DNA or locus
related to that particular phenotype.
 In epigenetics, various biochemical modifications are observed, one of the oldest of
those modifications is DNA Methylation(5mC). After that, various other biochemical
modifications like acetylation, phosphorylation, were observed. Acetylation of histone
is one of the most studied epigenetic markers, as it has profound effects on the human
body.
 Histone is a protein that provides structural support to a chromosome. For very long
DNA molecules to fit into the cell nucleus. Allfrey V.G et al were among the first people
who observed acetylation of histone in the salivary gland chromosome of Chironomus
thummi. In 1998, scientists Paola Gavazzo et al discovered the relation between
acetylation of histone and its ability to open chromatin.

4.  Acetylation of histone neutralizes positive charges of lysins and consequently decreases
histone–DNA interactions .The enzymes responsible for these are called Histone Acetyl
Transferases (HATs).
 Proteins that deacetylase the acetylated histones, known as Histone Deacetylase (HDAC).
HDAC mainly works opposite to HATs and they work simultaneously to maintain the DNA-
Histone interaction.

5. Histone and Nucleosome
 In eukaryotic cells, their genetic data is stored by the coding of DNA molecules. Histone
is the main protein that helps to pack DNA hierarchically up to 2x10-5 times smaller
than its length. DNA, with help of histone, forms a complex known as Chromatin.
 Histone proteins are divided into H2A, H2B, H3, and H4. All of these proteins together
form a nucleosome, which is the basis of the structure of chromatin.
 Nucleosome is a heterotypic tetramer of H3 and H4 [(H3-H4)2] with a dimer of H2A
and H2B [(H2A-H2Nb)] in the form of [(H2A-H2B)(H3-H4)2(H2A-H2B)].
 Nearly 147 base pair length of DNA then gets wrapped in the histone octamer in a 1.7
superhelical turn. These nucleosomes are then connected by a DNA linker of variable
length that forms a 10-nm beads-on-a-string array.

6. Histone Deacetylase
 In the structure of chromatin, two antagonistic sets of enzymes, histone acetyl
transferases (HATs) and histone deacetylases (HDACs) reversibly control the acetylation
and deacetylation of histone.
 HAT acetylases the ε-amino groups located on the N terminal of lysine in every major
in-vivo histones by use of acetyl CoA as a cofactor.
 HDAC class of enzymes works opposite to HATs, and reverses the acetylation of the N-
terminal of lysine, thus restoring the positive charge on lysine. This leads to the
stabilization of the local chromatin structure

7. Classification of HDAC
 HDAC classes of enzymes can be seen from yeast to humans. In humans, all
total of 18 different types of HDAC enzymes can be seen, which are classified
into 4 classes and two families
 Classical families of HDAC, which include Class I, II, and IV are zinc-dependent
amidohydrolases. They are also sensitive to Zn2+ dependent chelating agents.
HDAC Class Members Size(kD) Dependency
Class I HDAC 1,2,3,8 22-25 Zn2+ dependent
Class IIa HDAC4, 5, 7, 9 120-135 Zn2+ dependent
Class IIb HDAC6, 10 Zn2+ dependent
Class III SIRT 1-7 40-50 NAD+-dependent
Class IV HDAC 11 Zn2+ dependent

8.  Class I enzymes, which includes HDAC 1,2,3,
and 8 are yeast transcriptional regulator RPD3.
They are exclusively localized in the nucleus
and are expressed in most cells.
 Class II enzymes which include HDAC 5,6,7,9
and 10, are also homologous to yeast
deacetylase HDA1. Class II HDACs can shuttle
in and out from the nucleus to respond to
cellular signals. Class II enzymes are
restrictive in expression patterns.
 Silent family, which includes Class III has
recently identified sirtuin-based enzymes.
They are closely related to Silent information
regulator 2 (Sir2) proteins of yeast, and are
NAD+ dependent enzymes. Zn2+ dependent
HDAC inhibitors do not work on class III
HDACs.
 Class IV is a recently discovered HDAC class,
which is the only member is HDAC 11. It is
discovered in 2001 by scientists Lin Gao,
Maria A. Cueto, Fred Asselbergs, and Peter
Atadja. HDAC 11 shares residues in catalytic
core region with both Class I and Class II.
HDAC 11 has distinctive features to be
considered its own Class.

9. Discovery of HDAC11
 Histone Deacetylase 11, or HDAC11 is first discovered by Peter Atadja et al on 2001-
2002.
 HDAC11 is the only member of Class IV HDAC enzymes. HDAC11 was first cloned in-vitro
from Normal dermal human fibroblast cells using RT-PCR technology.
 HDAC11 has 347 amino acid residues and weighs nearly 39 kDa. HDAC11 gene is situated
at Chromosome 3 in human
 Scientist Atadja et al, grew normal dermal human fibroblast cells in Dulbecco’s
modified Eagle’s medium. In this culture, total of 293 cells were grown. From these
dermal fibroblast cells, cDNA is being extracted. From these cDNA, HDAC11 cDNA are
cloned.
 For cloning on this Reverse transcription-PCR was employed to generate the HDAC11
coding region. Sequence of the PCR primers are: forward:5’-
GAGGATCCACCATGCTACACACAACCCAGCTG-3’ and reverse: 5’-
GCGTCTAGACTACTTGTCATCGTCGTCCTTGTAATCAGCCCGGGGCACTGCAGGGGGAAG- 3’ .
 Various types of in-vitro assay are then done to confirm the production of histone
deacetylase, and then finally a novel HDAC is being identified by performing searches
using the yeast HOS3 protein as the query sequence. HOS3 is a member of the HDAC
family, which contains deacetylase functions shared by both Class I and II HDACs.

10. Chemistry of HDAC11
 The HDAC11 has an open reading frame of 347 residues of amino acids, and 39kDA of
molecular mass.
 The position of the HDAC11 gene is in chromosome 3 at position 3p25.2, with a length
of 25kb expressing 9 exons and 8 introns.
 A comparison of the amino acid sequence between HDAC11 and other classes of HDACs
shows that the sequence is not much homologues to known HDACs, and well as HOS3
yeast protein.
Predicted 3D-Structure of HDAC11( source: AlphaFold)

11. Sequence of HDAC11
The proper sequence of the HDAC11 is still not confirmed, but an approximate sequence is
given below (source Alphafold)
DBREF XXXX A 1 347 UNP Q96DB2 HDA11_HUMAN 1 347
SEQRES 1 A 347 MET LEU HIS THR THR GLN LEU TYR GLN HIS VAL PRO GLU
SEQRES 2 A 347 THR ARG TRP PRO ILE VAL TYR SER PRO ARG TYR ASN ILE
SEQRES 3 A 347 THR PHE MET GLY LEU GLU LYS LEU HIS PRO PHE ASP ALA
SEQRES 4 A 347 GLY LYS TRP GLY LYS VAL ILE ASN PHE LEU LYS GLU GLU
SEQRES 5 A 347 LYS LEU LEU SER ASP SER MET LEU VAL GLU ALA ARG GLU
SEQRES 6 A 347 ALA SER GLU GLU ASP LEU LEU VAL VAL HIS THR ARG ARG
SEQRES 7 A 347 TYR LEU ASN GLU LEU LYS TRP SER PHE ALA VAL ALA THR
SEQRES 8 A 347 ILE THR GLU ILE PRO PRO VAL ILE PHE LEU PRO ASN PHE
SEQRES 9 A 347 LEU VAL GLN ARG LYS VAL LEU ARG PRO LEU ARG THR GLN
SEQRES 10 A 347 THR GLY GLY THR ILE MET ALA GLY LYS LEU ALA VAL GLU
SEQRES 11 A 347 ARG GLY TRP ALA ILE ASN VAL GLY GLY GLY PHE HIS HIS
SEQRES 12 A 347 CYS SER SER ASP ARG GLY GLY GLY PHE CYS ALA TYR ALA
SEQRES 13 A 347 ASP ILE THR LEU ALA ILE LYS PHE LEU PHE GLU ARG VAL
SEQRES 14 A 347 GLU GLY ILE SER ARG ALA THR ILE ILE ASP LEU ASP ALA
SEQRES 15 A 347 HIS GLN GLY ASN GLY HIS GLU ARG ASP PHE MET ASP ASP
SEQRES 16 A 347 LYS ARG VAL TYR ILE MET ASP VAL TYR ASN ARG HIS ILE
SEQRES 17 A 347 TYR PRO GLY ASP ARG PHE ALA LYS GLN ALA ILE ARG ARG
SEQRES 18 A 347 LYS VAL GLU LEU GLU TRP GLY THR GLU ASP ASP GLU TYR
SEQRES 19 A 347 LEU ASP LYS VAL GLU ARG ASN ILE LYS LYS SER LEU GLN
SEQRES 20 A 347 GLU HIS LEU PRO ASP VAL VAL VAL TYR ASN ALA GLY THR
SEQRES 21 A 347 ASP ILE LEU GLU GLY ASP ARG LEU GLY GLY LEU SER ILE
SEQRES 22 A 347 SER PRO ALA GLY ILE VAL LYS ARG ASP GLU LEU VAL PHE
SEQRES 23 A 347 ARG MET VAL ARG GLY ARG ARG VAL PRO ILE LEU MET VAL
SEQRES 24 A 347 THR SER GLY GLY TYR GLN LYS ARG THR ALA ARG ILE ILE
SEQRES 25 A 347 ALA ASP SER ILE LEU ASN LEU PHE GLY LEU GLY LEU ILE
SEQRES 26 A 347 GLY PRO GLU SER PRO SER VAL SER ALA GLN ASN SER ASP
SEQRES 27 A 347 THR PRO LEU LEU PRO PRO ALA VAL PRO

12. Characteristics of HDAC11
 In HDAC11 its catalytic site presents a conserved funnel-shaped
channel structure that accommodates a modified lysine residue, the
invariant catalytic residues around the Zn2+ ion at the bottom of the
funnel, and 4 loops of variable length and structure at the entrance of
the funnel that interact with protein regions and might be involved in
substrate recognition .
 The histidine 142 and 143 are key for HDAC activity, catalyzing the
hydrolysis of the acyl groups. Changing histidine 142 and 143 to
alanines generates catalytically inactive mutants of both deacetylase
and demyrstoilase HDAC11 enzymatic activities.
 The catalytical channel structure has a conserved funnel shape in all
HDACs; this funnel is enlarged by amino acid substitutions in HDAC11,
this increased size of HDAC11 allows it to accommodate bigger acyl
groups.

13. Biological and Clinical Activities of HDAC11
 In Humans body, HDAC11expression was originally described to be restricted to the
brain, kidney, testis, heart, and skeletal muscle. In WBC, it has increased activity as an
Interleukin-10 inhibitor, which influences with the immune system.
 HDAC11 activity goes beyond its activity on Histone, it can deacetylate E2F1 and E2F4
transcription factor which regulates their binding affinity to the adrenodoxin reductase
tumor suppressor gene (ARH1) promoter and controls their expression in breast cancer
cells.
 HDAC11 has ability to deacetylase long-chain fatty acids like decanoyl- or dodecanoyl-
peptides, myristoyl- or octanoylpeptides, etc.
 In the Human body, testis has the highest level of HDAC11 expression, which suggest
that sex-specific expression of HDAC11 also occurs. During zygote fertilization, HDAC11
expression is highest in sperm and almost absent in both female metaphase II (MII) eggs
or fertilized zygotes, suggesting that HDAC11 might be a paternally provided mRNA that
controls gene expression before egg-to zygote transition.
 Brain is also an organ that has a high expression of HDAC11. At the cellular level, the
HDAC11 protein is mainly localized in the nuclei of mature oligodendrocytes, the
myelin-producing cells. HDAC11 helps in the differentiation of the oligodendrocytes,
and promotes the myelin basic protein and proteolipid formation.

14. Expression of HDAC11 in Humans

15. HDAC11 and Tumor
 In pancreatic neuroendocrine tumors , that HDAC11 is highly expressed in tumors
compared with control tissues, especially in tumors with a histological grade of G3.
 HDAC11 has a high expression on the testis as well as other sex organs. Studies show,
that HDAC11 is overexpressed in prostate (PC-3), ovarian (SK-OV-3), breast cancer
(MCF-7), and testis cell lines, this leads to the stopping of apoptosis and maintains the
metabolism of tumor cells.
 In digestive system, HDAC11 ia strongly expressed in colon cancer. The increased
number of the mir-45 by macrophages phagocytizing exosomes derived from
colorectal cancer cells leads to inhibited expression of the HDAC11, which leads to
increased IL-10 secretion, which finally leads to cancer growth.

16. HDAC Inhibitors
 HDAC Inhibitors are novel drugs, which have been recently used as an
epigenetic or non-epigenetic regulator of carcinomas by inducing
apoptosis, and cell cycle arrest in cancer cells.
 HDACi can be broadly classified into at least four classes-
hydroxamates, cyclic peptides, aliphatic acids, and benzamides.
 Trichostatin A(TSA) was the first natural hydroxamate found to inhibit
HDACs. Vorinostat is structurally similar to TSA and was the first FDA-
approved HDAC inhibitor for the treatment of relapsed and refractory
Cutaneous T-Cell Lymphoma.
 General mechanism of action of most HDACi are to alter gene expression. and
changes to non-histone proteins via regulation at the epigenetic and post-
translational modification levels.

17. Conclusion
 Histone Deacetylase 11 is a novel HDAC discovered by Peter Atadja et
al on 2001-2002.
 It is the only member of Class IV HDAC.
 The clinical effects of HDAC11 are still under various studies, and it is
a novel target for various diseases including cancer.
 HDAC11 may open a vast field for various anti-cancer drugs

18. References
 C. H. Waddington, The Epigenotype, International Journal of Epidemiology,
Volume 41, Issue 1, February 2012, Pages 10–13,
https://doi.org/10.1093/ije/dyr184
 Gao L, Cueto MA, Asselbergs F, Atadja P. Cloning and functional
characterization of HDAC11, a novel member of the human histone
deacetylase family. J Biol Chem. 2002 Jul 12;277(28):25748-55. doi:
10.1074/jbc.M111871200. Epub 2002 Apr 10. PMID: 11948178.
 Gavazzo P, Vergani L, Mascetti GC, Nicolini C. Effects of histone acetylation
on chromatin structure. J Cell Biochem. 1997 Mar 1;64(3):466-75. doi:
10.1002/(sici)1097-4644(19970301)64:3<466::aid-jcb13>3.0.co;2-e. PMID:
9057104
 Deubzer HE, Schier MC, Oehme I, Lodrini M, Haendler B, Sommer A, Witt O.
HDAC11 is a novel drug target in carcinomas. Int J Cancer. 2013 May
1;132(9):2200-8. doi: 10.1002/ijc.27876. Epub 2012 Oct 25. PMID: 23024001.
 HDAC11: a rising star in epigenetics , Shan-Shan Liu, Fei Wu Yue-Mei Jin Wei-
Qin Chang Tian-Min Xu , https://doi.org/10.1016/j.biopha.2020.110607

19. THANK YOU