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The Authors Journal compilation 2009 Biochemical Society
Essays Biochem. (2009) 46, 95–110; doi:10.1042/BSE0460007
Polyamine analogues targeting
epigenetic gene regulation
Yi Huang*, Laurence J. Marton†, Patrick M.
Woster¶ and Robert A. Casero, Jr*1
*The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins,
The Johns Hopkins University School of Medicine, Bunting ◊ Blaustein
Cancer Research Building, 1650 Orleans Street, Baltimore, MD 21231,
U.S.A., †Progen Pharmaceuticals, Redwood City, CA 94065, U.S.A.,
and ¶Department of Pharmaceutical Sciences, Wayne State University,
Detroit, MI 48202, U.S.A.
Over the past three decades the metabolism and functions of the polyamines have been actively pursued as targets for antineoplastic therapy. Interactions between cationic polyamines and negatively charged nucleic acids play a pivotal role in DNA stabilization and RNA processing that may affect gene expression, translation and protein activity. Our growing understanding of the unique roles that the polyamines play in chromatin regulation, and the discovery of novel proteins homologous with specifi c regulatory enzymes in polyamine metabolism, have led to our interest in exploring chromatin remodelling enzymes as potential therapeutic targets for specifi c polyamine analogues. One of our initial efforts focused on utilizing the strong affi nity that the polyamines have for chromatin to create a backbone structure, which could be combined with active-site-directed inhibitor moieties of HDACs (histone deacetylases). Specific PAHAs (polyaminohydroxamic acids) and PABAs (polyaminobenzamides) polyamine analogues have demonstrated potent inhibition of the HDACs, re-expression of p21 and significant inhibition 1To whom correspondence should be addressed (email [email protected]). 0046-0007 Casero.indd 95 10/9/09 4:38:43 PM Essays in Biochemistry volume 46 2009 of tumour growth. A second means of targeting the chromatin-remodelling enzymes with polyamine analogues was facilitated by the recent identifi cation of fl avin-dependent LSD1 (lysine-specifi c demethylase 1). The existence of this enzyme demonstrated that histone lysine methylation is a dynamic process similar to other histone post-translational modifi cations. LSD1 specifi cally catalyses demethylation of mono- and di-methyl Lys4 of histone 3, key positive chromatin marks associated with transcriptional activation. Structural and catalytic similarities between LSD1 and polyamine oxidases facilitated the identifi cation of biguanide, bisguanidine and oligoamine polyamine analogues that are potent inhibitors of LSD1. Cellular inhibition of LSD1 by these unique compounds led to the re-activation of multiple epigenetically silenced genes important in tumorigenesis. The use of these novel polyamine-based HDAC or LSD1 inhibitors represents a highly promising and novel approach to cancer prevention and therapy.
Polyamines are naturally occurring polycationic alkylamines that are essential for eukaryotic cell growth. By virtue of their positively charged amine groups, polyamines interact with negatively charged DNA, RNA, proteins and phospholipids to change their structure and conformation. The enzymes controlling polyamine metabolism and intracellular concentrations are highly regulated and can rapidly react to changing environmental conditions. Intracellular polyamine levels and metabolism are frequently dysregulated in cancer and other hyperproliferative diseases, thus making polyamine function and metabolism attractive targets for therapeutic intervention [1,2]. The key polyamine biosynthetic enzyme, ODC (ornithine decarboxylase), has long been thought to be a marker of carcinogenesis and tumour progression [3]. Inhibiting polyamine biosynthesis by specifi cally targeting ODC as an anticancer strategy has yet to demonstrate signifi cant clinical success, but it has demonstrated considerable promise as a strategy for cancer chemoprevention [4]. Recently, more focus has been directed towards the development of polyamine analogues designed to mimic the regulatory roles of natural polyamines but to have altered function. A number of synthetic polyamine analogues have exhibited encouraging effects against tumour growth in both cell culture and animal studies and several hold promise as chemotherapeutic agents [5].
There are considerable data demonstrating that chromatin is a major target for the natural polyamines and polyamine-based drugs [6–8]. Therefore we have attempted to use this property to advance the hypothesis that specifi c polyamine analogues could target the chromatin remodelling enzymes, includ-ing the HDACs (histone deacetylases) and the newly identifi ed histone LSD1 (lysine-specifi c demethylase 1). These enzymes, among others, are responsible for normal gene regulation, and in a variety of disease processes their activity may lead to aberrant silencing of important tumour suppressor genes. As aber-rant epigenetic silencing of tumour suppressor genes is a common occurrence The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 96 10/9/09 4:38:43 PM Y. Huang and others in the development of cancer, this strategy holds considerable promise for the treatment of neoplastic disease, and the present chapter will discuss the most recent fi ndings in the fi eld [9].
Polyamines are critical for eukaryotic cell growth and thus maintenance of appropriate intracellular concentrations via a highly regulated interplay between biosynthesis, catabolism, uptake and excretion is required for normal function (Figure 1). Two major regulatory enzymes of polyamine biosynthesis are ODC and AdoMetDC (S-adenosylmethionine decarboxylase). The regulatory protein Az (antizyme) facilitates the degradation of ODC and down-regulates the transport of polyamines into the cell, and thus is considered to be dedicated principally to the feedback regulation of Figure 1. Polyamine metabolism in mammals
The major regulatory enzymes of polyamine biosynthesis are ODC and AdoMetDC. ODC
forms putrescine from L-ornithine and is the fi rst rate-limiting step in polyamine biosynthe-
sis. The regulatory protein Az can facilitate degradation of ODC and negatively regulate the
eukaryotic polyamine transport system. AdoMetDC forms decarboxylated S-adenosylmethionine
(DC-AdoMet) from S-adenosylmethionine, and DC-AdoMet acts as an aminopropyl donor.
Spermidine synthase and spermine synthase transfer the aminopropyl group from DC-AdoMet
to putrescine or spermidine for the synthesis of spermidine, spermine and MTA (5′-deoxy-5′-m
ethylthioadenosine) respectively. After acetylation of spermine and spermidine by SSAT to form
N1-acetylspermine and N1-acetylspermidine respectively, acetyl derivatives are then cleaved into
3-aceto-aminopropanal, the ROS H O and spermidine and putrescine respectively, through the
action of FAD-dependent APAO. SMO is a highly inducible FAD-dependent enzyme that directly oxidizes spermine to produce spermidine, 3-aminopropanal and H O The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 97 10/9/09 4:38:43 PM Essays in Biochemistry volume 46 2009 polyamine levels [10]. Polyamine catabolism was initially thought to be a two-step procedure regulated by the rate-limiting enzyme SSAT (spermidine/spermine N1-acetyltransferase), which provides substrate for the generally constitutively expressed APAO (N1-acetylpolyamine oxidase) [11]. After acetylation of spermine and spermidine by SSAT to form N1-acetylspermine and N1-acetylspermidine respectively, acetyl derivatives are then cleaved into 3-acetamidopropanal, the ROS (reactive oxygen species) H O , and spermidine and putrescine respectively, through the action of FAD-dependent APAO. However, recent studies from our laboratory and others have demonstrated that a variably spliced human SMO (spermine oxidase) efficiently uses unacetylated spermine as a substrate, and that this enzyme is inducible by specifi c polyamine analogues [12–15]. These fi ndings indicate the existence of a more complex polyamine catabolic pathway in the regulation of polyamine homoeostasis than originally thought.
Epigenetic regulation of gene expression
Epigenetic modification of chromatin is a major regulator of gene expression. Epigenetic modifi cations refer to heritable changes in chromatin/DNA that are not due to changes in primary sequence. These include a variety of modifi cations of the histone proteins and methylation of cytosine residues in DNA. The histone proteins are the major packaging proteins of eukaryotic DNA. The eukaryotic genome requires packaging of DNA both for structural purposes, as a means of fi tting 2 m of DNA into the nucleus, and as one mechanism for the regulation of gene expression. Two of each of the core histone proteins, H2A, H2B, H3 and H4, are assembled into the nucleosome, around which 146 bp of DNA are wound. This nucleosome is the basic packaging unit of eukaryotic chromatin and the density of nucleosomes and the affi nity of the individual nucleosomes on any stretch of DNA determine the accessibility of the gene to various factors, including the basic transcriptional machinery. Importantly, in cancer, aberrant epigenetic silencing of gene expression, including tumour suppressor genes, is a common occurrence [9].
There are numerous possible modifications of histone tails, including acetylation, methylation, ubiquitination, phosphorylation, SUMOylation and ribosylation, each of which can affect the expression of genes [16]. The spe-cifi c modifi cation of histones determines, in part, which regions of the genome are in an open and transcriptionally active confi rmation and which are closed and transcriptionally inactive. The most studied of the histone modifi cations are acetylation/deacetylation and methylation. Acetylated histones are typi-cally associated with active gene transcription. However, histone methylation can either be activating or inhibitory with respect to transcription, depend-ing on the specifi c residue methylated. Histones may be methylated on either lysine (K) or arginine (R) residues, and the methylation status of key histone lysine residues, such as H3K4, H3K9, H3K27, H3K36, H3K79 and H4K20, represent specifi c epigenetic marks that are associated with transcriptional The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 98 10/9/09 4:38:44 PM Y. Huang and others regulation. Although the dynamic nature of histone acetylation, mediated through the counterbalancing activity of HATs (histone acetyltransferases) and HDACs, has been known for some time [17], only recently has a similar dynamic regulation of histone methylation been demonstrated. Shi et al. [18] reported the discovery of the fi rst enzyme able to specifi cally demethylate Lys4 of histone H3. The newly identifi ed protein was therefore named LSD1 (lysine-specifi c demethylase; BHC110) [18]. Subsequent to the discovery of LSD1, a family of Jmj C (Jumonji C) domain-containing histone demethylases was also identifi ed, thus expanding the number of known proteins involved in chromatin remodelling [19]. These fi ndings fi rmly establish that histone methylation is a dynamic process under enzymatic control, similar to the other post-translational histone modifi cations, and suggest that this modifying enzyme may also be a rational target for therapeutic intervention [20].
Exploiting polyamine structure to target aberrantly
silenced genes
The incorporation of a polyamine structure into the design of a putative drug offers several benefi ts as a targeting vehicle, particularly when chromatin is the target. A selective, energy-dependent polyamine transport system allows molecules resembling the general polyamine structure to be accumulated by cells, and the cationic nature of the polyamine backbone provides affi nity to the negatively charged chromatin. Several investigators have used the polyamine structure as a backbone to which various active moieties have been conjugated, including alkylating agents, DNA intercalators and other antiproliferative agents [21,22]. Delcros et al. [23] have tested the limits of polyamine transport with respect to size and types of molecules that can be attached to the polyamine backbone and still be effectively transported. The fi ndings of each of the above studies clearly indicate that the polyamine structure can be used effectively to transport specifi c active moieties into cells and in many cases, target chromatin. We recently attempted to build on this paradigm with a new generation of agents that target chromatin [25,26,36]. However, unlike previous attempts, our goal was not to damage chromatin, but rather to alter its regulation of gene expression.
Polyamine analogues as HDAC inhibitors
The growing interest in drugs that alter chromatin is based on the recognition
that epigenetic regulation of gene expression plays a critical role in the
aetiology and progression of cancer and, unlike gene mutations or loss,
epigenetic changes are, in theory, reversible [9]. Aberrant silencing of tumour
suppressors and other genes has been found in all cancers examined. One of
the major regulators of chromatin conformation, and hence gene expression,
is histone acetylation. As stated above, acetylation of histones is generally
associated with transcriptionally active chromatin, and activity of HDACs lead
to condensation of chromatin and inhibition of transcription. A number of
The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 99 10/9/09 4:38:44 PM Essays in Biochemistry volume 46 2009 class I/II HDAC inhibitors have been examined for their ability to re-express silenced genes [24]. Although several class I/II HDCA inhibitors have been synthesized and some are currently in clinical trial, virtually all of them have been designed to target primarily the zinc cofactor at the active site of the HDACs [24].
We have previously reported the use of various polyamine analogue struc- tures combined with active-site-directed inhibitor moieties of the class I/II HDACs [25,26]. This strategy has the advantage of using known structures that inhibit the HDACs, the hydroxamic acids and benzamides, combined with the high chromatin affi nity of the polyamine structure. Additionally, as tumour cells are known to transport and accumulate many of the polyamine analogues, the polyamine backbone offers the likelihood that these com-pounds would be readily transported into tumour cells. Specifi c members of the PAHA (polyaminohydroxamic acid) and PABA (polyaminobenzamide) polyamine analogues demonstrated potent inhibition of the class I/II HDACs in a cell-free system, and in treated leukaemia cells re-expression of the growth regulating CDK (cyclin-dependent kinase) inhibitor p21 was observed. Some of these analogues also signifi cantly inhibited tumour cell growth in vitro.
An additional advantage of using the polyamines as a backbone for HDAC inhibitors is that it provides a scaffold upon which it is possible to design mol-
ecules that possess selectivity for the individual HDACs (see Chapter 6 by
Woster). This possibility would be useful in the design of molecular tools to
study the effects of inhibiting the individual HDACs, and may provide a thera-
peutic advantage over existing non-selective inhibitors. One promising com-
pound that demonstrates some selectivity with respect to HDAC inhibition
was the compound designated 17 (Figure 2) in Varghese et al. [26]. The class II
HDAC6, in addition to having histone targets, is also capable of deacetylating
α-acetyltubulin. Compound 17 demonstrated potent functional in situ inhibi-
tion of HDAC6 resulting in a substantial increase in α-acetyltubulin in treated
cells. These data underscore the possibility of using the fl exibility allowed by
the polyamine structure to design selective inhibitors for each of the individual
class I/II HDACs.
Although considerable work remains to be done, the initial analysis of the polyamine analogue HDAC inhibitors of both the PAHA and PABA families shows considerable promise.
Targeting LSD1 for gene re-expression
As stated above, the discovery of LSD1 and the Jmj C domain-containing
demethylases indicated that histone methylation, like histone acetylation,
is a dynamic process. Structural analysis demonstrates that LSD1 is highly
conserved across species and consists of an N-terminal SWIRM (Swi3p/Rsc8c/
Moira) domain, a central protruding tower domain and a C-terminal amine
oxidase-like domain, containing a FAD-binding subdomain, which is highly
homologous with MAOs (monoamine oxidases) and the polyamine oxidases,
The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 100 10/9/09 4:38:44 PM Y. Huang and others Figure 2. Chemical structures of polyamine analogues
Compound 17 selectively inhibits HDAC6 activity and increases acetylated α-tubulin in HCT116
colorectal cancer cells. 1c and 2d are potent inhibitors of LSD1 activity and re-activate aberrantly
silenced genes in tumour cells. PG-11144 and PG-11150 polyamine analogues contain ten amines
and are a cis/trans pair with double bonds in the centre of their structure. Oligoamines competi-
tively inhibit LSD1 activity and re-activate aberrantly silenced genes in colorectal cancer cells.
SMO and APAO [18,27] (Figure 3). LSD1 catalyses the demethylation of mono- or di-methylated Lys4 of histone H3 (H3K4) by cleavage of the α-carbon bond of the substrate through an oxidative process with the reduction of FAD. FADH is re-oxidized by oxygen to produce H O , leading to the generation of an imine intermediate. The imine intermediate is subsequently hydrolysed to generate formaldehyde and the amine of lysine (Figure 4). Despite the similarity of structure and chemistry between these amine oxidases, LSD1 demonstrates entirely different biological activity and cellular localization than do the MAOs (Table 1). MAOs, including two isoforms MAO A and MAO B, are bound to the outer mitochondrial membrane [28]. APAO is a peroxisomal enzyme, whereas SMO is found in both the cytoplasm and nucleus [14]. Both APAO and SMO are FAD-dependent enzymes The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 101 10/9/09 4:38:45 PM Essays in Biochemistry volume 46 2009 Figure 3. Structure and domain organization comparison of LSD1 and polyamine
oxidases
(A) LSD1 is 852 amino acids long and consists of an N-terminal SWIRM domain, a central
protruding tower domain and a C-terminal AOL (amine oxidase-like) domain that contains a
FAD-binding catalytic subdomain. Lys661 (K661) of LSD1 is a critical residue at the FAD-binding
site that is associated with the N5 atom of FAD through a hydrogen bond. The primary
splice variant of human SMO codes for a protein of 511 amino acids, and Lys367 (K367) at the
C-terminal is the key residue for FAD association. The predominant human splice variant of
APAO contains 551 amino acids, and Lys322 (K322) is important for FAD binding. (B) Structural
comparison of the FAD-associated catalytic centre of LSD1 and polyamine oxidases. The catalytic
domains of LSD1, SMO and APAO possess over 60% similarity in amino acid sequences.
that oxidize polyamine substrates and produce H O . The structural and catalytic similarities of these FAD-dependent oxidases has been instructive in understanding the basic biology of FAD-dependent oxidases, as well as in the search for effective inhibitors that can interact with LSD1.
Figure 4. Mechanism of histone demethylation by LSD1
LSD1 catalyses the FAD-dependent demethylation of mono- (R=H) or di-methyl (R=CH ) Lys4
of histone 3 through transferring two hydrogen atoms from methylated H3K4 to FAD with the resultant reduction of oxygen to H O . The imine intermediate is then hydrolysed to an unstable carbinolamine that subsequently degrades to release formaldehyde.
The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 102 10/9/09 4:38:45 PM Y. Huang and others Table 1. Comparison of biological functions between amine oxidases and
Cytoplasm, nucleus Cellular function Linking LSD1-suppressed gene expression to the role of LSD1
in tumorigenesis
LSD1 is a member of a multiprotein co-repressor complex that includes CoRest,
HDAC1/2 and BHC80. Several recent studies demonstrate that inhibition
of LSD1 by siRNA (small interfering RNA) or pharmacological inhibition
changes global and promoter-specifi c H3K4me2 (dimethylated H3K4) levels
and increases expression of some known LSD1/CoREST-target genes. For
example, Shi et al. [18] demonstrated an up-regulation of neuron-specifi c M4
AchR, SCN1A-3A and the CDK inhibitor p57KIP2 in LSD1 RNAi (RNA
interference)-treated HeLa cells. Lee et al. [27] reported an increase in global
H3K4me2, as well as transcriptional de-repression of two LSD1 target genes,
Egr1 and the pluripotent stem cell marker Oct4, in P19 EC cells treated with
a non-specifi c MAO inhibitor. A recent study demonstrated that knockout of
LSD1 in embryonic stem cells induces progressive loss of DNA methylation
and a decrease in DNA methyltransferase 1 stability and protein levels [29].
These interesting findings demonstrate a previously unknown mechanistic
interaction between histone demethylase and DNA methyltransferase.
DNA promoter hypermethylation frequently acts in concert with histone modifi cations that result in decreased chromatin-activating marks, such as H3K4me (monomethylated H3K4), resulting in increased repressive marks such as H3K9me and H3K27me, and in the aberrant silencing of specifi c genes [30]. Since the discovery of LSD1 as an important demethylase of the key activating mark H3K4, the potential association of LSD1 activity with tumori-genesis has been intensively investigated. A number of recent studies indicate that an alteration in the function of LSD1 has a role in cancer. For example, The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 103 10/9/09 4:38:46 PM Essays in Biochemistry volume 46 2009 high-level LSD1 expression has been linked to an increased risk of prostate cancer recurrence, suggesting a tumour-promoting role for LSD1 [31]. In another study, LSD1 was shown to possess a pro-oncogenic activity through its regulation of pro-survival gene expression and p53 transcription in human breast cancer cells [32]. Bradley et al. [33] reported that induction of LSD1 is one of the early responses to chemical carcinogens in HMECs (human mam-mary epithelial cells), and that it may affect the expression of multiple genes critical in early-stage mammary oncogenic transformation. Very recently, Schulte et al. [34], demonstrated that a non-specifi c MAO inhibitor is effec-tive in inducing expression of genes associated with differentiation in neurob-lastoma cells, and that the inhibitor can cause signifi cant in vivo inhibition of tumour growth. These studies have established LSD1 as an important link to the development and progression of cancer and provide a rationale for devel-oping LSD1 inhibitors as a target for therapeutic intervention.
Identifi cation of polyamine analogues as effective LSD1 inhibitors.
Human LSD1 shares 20% similarity in overall structure with that of other
FAD-dependent amine oxidases. Specifi cally, the catalytic domains of LSD1
and SMO are over 60% similar in amino acid sequence (Figure 3). This
similarity suggests that specifi c polyamine analogues may function as effective
inhibitors of LSD1 (Table 2).
Although the natural polyamines or acetylpolyamines are not substrates of LSD1 [18], the strong association of polyamines with chromatin and the structural similarity between the polyamines and the lysine tails of histones suggest that polyamines and/or polyamine analogues may alter the activity of LSD1 and other chromatin modifi ers. In our previous studies we discovered that specifi c polyamine analogues function as potent inhibitors of purifi ed polyamine oxidases [15,35]. Since the active site of LSD1 is closely related to that of SMO and APAO, and because guanidines have been shown to inhibit the activity of structurally related polyamine oxidases, we sought to determine whether a small library of bisguanidine and biguanide polyamine analogues (Figure 2) functioned as effective inhibitors of LSD1. Most of these compounds were found to inhibit the demethylase activity of recom-binant LSD1 by >50% at concentrations less than 1 μM [36]. The two most Table 2. Inhibitory effects of polyamine analogues on the activity of
recombinant polyamine oxidases, LSD1 and tumour cell growth
−, No effect; + to +++, modest to potent inhibition.
Polyamine
The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 104 10/9/09 4:38:46 PM Y. Huang and others potent analogues, 1c [1,11-bis(N2,N3-dimethyl-N1-guanidino)-4,8-diaza-
undecane] and 2d (1,15-bis{N5-[3,3-(diphenyl)propyl]-N1-biguanido}-4,12-di-
azapentadecane), exhibited non-competitive inhibition kinetics, suggesting that
these compounds probably bind to LSD1 at a site other than at the active site.
The possible mechanisms of action include the fact that these LSD1 inhibitors
may block FAD from associating with its binding site, or the fact that these
inhibitors might induce a conformational change in LSD1, such that LSD1 is
no longer able to bind to its histone lysine substrate correctly. It is, however,
possible that the enzymatic kinetics obtained when using recombinant LSD1
and a short peptide as a substrate in a cell-free system may not be representa-
tive of the interaction of the inhibitor and the nucleosome in association with
the LSD1–CoRest–HDAC complex in situ.
A class of long-chain polyamine analogues known as oligoamines has also been found to potently inhibit APAO or SMO (Table 2), suggesting that these analogues may also inhibit LSD1 [36]. Among others, we tested two cis/trans oligoamine isomers, PG-11144 and PG-11150 (Figure 2), for their ability to inhibit LSD1 [36] These oligoamines exhibit competitive-inhibition kinetics, suggesting that the oligoamines may directly compete with substrate at the active site in a manner different than seen for the bisguanidine and bigua-nide analogues. This new class of polyamine analogue LSD1 inhibitors offers another promising avenue of investigation.
It should be noted that the precise mechanism of inhibition of LSD1 by the polyamine analogues remains unclear. Ongoing crystallographic analysis should facilitate a better understanding of the molecular and structural basis of LSD1 inhibition by polyamine analogues, and perhaps provide insight into the design of more effective inhibitors [37].
Inhibition of LSD1 by novel polyamine analogues reactivates
silenced genes in cancer cells
To determine whether the in vitro inhibition of LSD1 activity by polyamine
analogues translated into a cellular response, the effects of polyamine analogues
as LSD1 inhibitors on global H3K4me status were examined in multiple
human cancer cell lines, including colorectal, breast, lung and leukaemia.
Exposure of cancer cells to these polyamine analogues leads to increased global
H3K4me2 and H3K4me1, with no change in H3K4me3 (trimethylated H3K4)
and H3K9me2 [36,38]. The promoter region of H3K4me2 is usually associated
with open chromatin and active transcription, and the occupancy of H3K4me2
was found to be at low levels in the promoters of a number of frequently DNA
hypermethylated and epigenetically silenced genes important in tumorigenesis
[30]. A number of such silenced genes have been identifi ed in colorectal cancer
cell lines, such as HCT116 and RKO. These genes include members of the
WNT signalling pathway antagonists, SFRPs (secreted frizzle-related protein)
family, GATA family transcription factors, the mismatch repair gene MLH1,
the cell-cycle regulator CDKN2A, and the tissue invasion regulator TIMP3
The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 105 10/9/09 4:38:46 PM Essays in Biochemistry volume 46 2009 (tissue inhibitor of metalloproteinase 3) [30]. Treatment of HCT116 cells with
1c or 2d for 48 h resulted in the re-expression of three members of the SFRP
family, SFRP1, SFRP4 and SFRP5, as well as of the GATA5 transcription
factor [36]. Similarly, treatment with PG-11144 or PG-11150 for 24 h led to
the re-expression of SFRP1 and SFRP2 [38]. Leukaemia cells treated with 2d
resulted in increased global H3K4me2 and the re-expression of E-cadherin, an
important tumour suppressor gene [39].
Chromatin immunoprecipitation analysis demonstrated that polyamine analogue-induced gene re-expression in HCT116 cells is closely associated with increased active histone marks H3K4me1/me2 and acetyl-H3K9, and decreased repressive marks H3K9me1/me2 [36,38]. However, no change of H3K4me3 levels were detected after treatment with the polyamine analogues, suggesting that these compounds specifi cally target LSD1 rather than other histone demethylases such as the Jmj C histone demethylases that are capable of demethylating H3K4me3 [19]. Some other hallmarks of silenced chromatin, such as H3K9me3 and PcG (polycomb) group protein-mediated H3K27 meth-ylation, remain unchanged in the promoter regions of the analogue-activated genes after treatment with LSD1 inhibitors. These results are similar to the chromatin state of HCT116 treated with the DNA methylation inhibitor DAC (5-aza-2′-deoxycytidine) [40].
As noted above, CpG island hypermethylation frequently acts in concert with abnormal histone mark activities in silencing genes. Interestingly, the re-expression of aberrently silenced genes by our unique polyamine analogues occurs without wholesale changes in the methylation status of CpG islands of the gene examined. Similar results were observed in silenced genes that were reactivated by inhibition of the class III HDAC, SIRT1 (sirtuin 1) [41]. These results indicate that treatment with LSD1 inhibitors alone is suffi cient to produce gene re-expression, even when dense promoter DNA methylation is maintained.
It is possible that the polyamine analogues have effects other than inhi- bition of LSD1 that lead to gene re-expression. To address this issue, we
compared the effects of the inhibition of LSD1 with the analogues 1c and 2d
with those induced by an RNAi-mediated knockdown in LSD1 expression
in HCT116 cells. LSD1 depletion by RNAi was accompanied by increased
H3K4me2 at the promoters of re-activated genes, and resulted in modest re-
expression of the examined genes [36]. We found that pharmacological inhi-
bition of LSD1 with the analogues was more effective than was RNAi with
respect to re-expression of silenced genes, which may refl ect inherent differ-
ences in chromatin structure resulting from inhibitor–LSD1 complexes com-
pared with RNAi-induced decreases in LSD1 protein.
Combination of LSD1 inhibitors with other agents targeting
epigenetic regulation of gene expression
Combination chemotherapy is an important strategy in modern cancer
treatment, frequently having the advantage of allowing for lower and
The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 106 10/9/09 4:38:46 PM Y. Huang and others better-tolerated doses of individual chemotherapeutic agents, while at the same time improving the overall response as compared with when the agents are used alone. The combination of DNA methyltransferase and HDAC inhibitors has demonstrated synergistic effects in re-expressing epigenetically silenced genes in cultured cancer cells, and has produced clinical responses in patients with leukaemias [42,43]. Our latest studies demonstrate that the combination of low-dose oligoamines with DAC results in synergistic expression of the SFRP2 gene [38]. This result suggests that the combination of LSD1 inhibitors and DNA methylation inhibitors can collaborate in the re-expression of specifi c silenced genes and may provide a useful strategy for the potential clinical utility of these two agents, each of which targets different epigenetic regulatory enzymes.
Increasing knowledge regarding the molecular mechanisms of polyamine metabolism in cancer cells that has accumulated over the last three decades has provided unique opportunities for the development of many promising therapeutic agents. Despite the somewhat disappointing results obtained from clinical trials of the early polyamine biosynthesis inhibitors, polyamine metabolism remains a rational target for cancer therapy, and opportunities still exist for development of novel agents with better specifi city when targeting cancer cells and fewer side effects affecting normal tissues. The unique association of ‘superinduction' of polyamine catabolic enzymes with a cytotoxic response for certain polyamine analogues has been well elucidated and noted. The interaction of polyamine or polyamine-based analogues with nucleic acids has received considerable attention, although the exact mechanisms of this phenomenon are still being defi ned. Epigenetic regulation of gene expression has emerged as an important target for drug development in cancer therapy. Specific polyamine analogues have been identified as potent inhibitors of the HDACs. LSD1 is a newly identifi ed homologue of polyamine oxidase. Owing to its important activity in modifying chromatin and gene transcription, signifi cant attention has been focused on developing LSD1 inhibitors as an effective strategy in treatment of cancer and other diseases. Our recent fi ndings clearly suggest that novel polyamine analogues are powerful inhibitors of LSD1, both alone and in combination with other agents that target epigenetic silencing, and that they are capable of inducing re-expression of several aberrantly silenced genes important in tumorigenesis. The use of these compounds represents a new direction for drug development in cancer prevention and therapy.
• Polyamine effects on chromatin remodelling are important in the sta- bilization of DNA structure and in RNA processing and may affect diverse cellular functions including transcriptional regulation. The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 107 10/9/09 4:38:47 PM Essays in Biochemistry volume 46 2009 • Drug design based on polyamine structure, when combined with active site-directed inhibitor moieties of the HDACs, led to the successful development of specifi c HDAC inhibitors of the PAHA and PABA families. These inhibitors demonstrate potent inhibition of HDAC in tumour cells. • The recent identifi cation of fl avin-dependent LSD1, which specifi cally demethylates mono- and di-methyl Lys4 of histone 3, plays critical roles in regulating gene transcription. • The structural and catalytic similarities of LSD1 and polyamine oxi- dases have facilitated the identifi cation of a group of biguanide, bis-guanidine and oligoamine polyamine analogues as potent inhibitors of LSD1. • Inhibition of LSD1 alone and in combination with other agents target- ing epigenetic silencing are capable of inducing re-expression of a number of aberrantly silenced genes that are important in tumorigenesis. Casero, Jr, R.A. and Marton, L.J. (2007) Targeting polyamine metabolism and function in cancer
and other hyperproliferative diseases. Nat. Rev. Drug Discov. 6, 373–390
Wallace, H.M., Fraser, A.V. and Hughes, A. (2003) A perspective of polyamine metabolism.
Biochem. J. 376, 1–14
Pegg, A.E. (2006) Regulation of ornithine decarboxylase. J. Biol. Chem. 281, 14529–14532
Gerner, E.W. and Meyskens, Jr, F.L. (2009) Combination chemoprevention for colon cancer
targeting polyamine synthesis and infl ammation. Clin. Cancer Res. 15, 758–761
Seiler, N. (2005) Pharmacological aspects of cytotoxic polyamine analogs and derivatives for
cancer therapy. Pharmacol. Ther. 107, 99–119
Basu, H.S., Smirnov, I.V., Peng, H.F., Tiffany, K. and Jackson, V. (1997) Effects of spermine and
its cytotoxic analogs on nucleosome formation on topologically stressed DNA in vitro. Eur. J.
Biochem. 243, 247–258
Basu, H.S., Sturkenboom, M.C., Delcros, J.G., Csokan, P.P., Szollosi, J., Feuerstein, B.G. and
Marton, L.J. (1992) Effect of polyamine depletion on chromatin structure in U-87 MG human
brain tumour cells. Biochem. J. 282, 723–727
Sato, N., Ohtake, Y., Kato, H., Abe, S., Kohno, H. and Ohkubo, Y. (2003) Effects of polyamines on
histone polymerization. J. Protein Chem. 22, 303–307
Jones, P.A. and Baylin, S.B. (2007) The epigenomics of cancer. Cell 128, 683–692
10. Coffi no, P. (2001) Regulation of cellular polyamines by antizyme. Nat. Rev. Mol. Cell Biol. 2,
11. Pegg, A.E. (2008) Spermidine/spermine-N1-acetyltransferase: a key metabolic regulator. Am. J. Physiol. Endocrinol. Metab. 294, E995–E1010
12. Wang, Y., Devereux, W., Woster, P., Stewart, T., Hacker, A. and Casero, Jr, R. (2001) Cloning and characterization of a human polyamine oxidase that is inducible by polyamine analogue expo-
sure. Cancer Res. 61, 5370–5373
13. Vujcic, S., Diegelman, P., Bacchi, C.J., Kramer, D.L. and Porter, C.W. (2002) Identifi cation and characterization of a novel fl avin-containing spermine oxidase of mammalian cell origin. Biochem.
J. 367, 665–675
14. Murray-Stewart, T., Wang, Y., Goodwin, A., Hacker, A., Meeker, A. and Casero, Jr, R.A. (2008) Nuclear localization of human spermine oxidase isoforms: possible implications in drug response
and disease etiology. FEBS J. 275, 2795–2806
The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 108 10/9/09 4:38:47 PM Y. Huang and others 15. Wang, Y., Murray-Stewart, T., Devereux, W., Hacker, A., Frydman, B., Woster, P. and Casero, Jr, R. (2003) Properties of purifi ed recombinant human polyamine oxidase, PAOh1/SMO. Biochem.
Biophys. Res. Commun. 304, 605–611
16. Jenuwein, T. and Allis, C.D. (2001) Translating the histone code. Science 293, 1074–1080
17. Kuo, M.H. and Allis, C.D. (1998) Roles of histone acetyltransferases and deacetylases in gene
regulation. BioEssays 20, 615–626
18. Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J., Cole, P., Casero, R. and Shi, Y. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941–953
19. Klose, R.J., Kallin, E.M. and Zhang, Y. (2006) JmjC-domain-containing proteins and histone demethylation. Nat. Rev. Genet. 7, 715–727
20. Shi, Y. (2007) Histone lysine demethylases: emerging roles in development, physiology and dis- ease. Nat. Rev. Genet. 8, 829–833
21. Holley, J.L., Mather, A., Wheelhouse, R.T., Cullis, P.M., Hartley, J.A., Bingham, J.P. and Cohen, G.M. (1992) Targeting of tumor cells and DNA by a chlorambucil-spermidine conjugate. Cancer
Res. 52, 4190–4195
22. Phanstiel, O.I., Price, H.L., Wang, L., Juusola, J., Kline, M. and Shah, S.M. (2000) The effect of polyamine homologation on the transport and cytotoxicity properties of polyamine-(DNA-
intercalator) conjugates. J. Org. Chem. 65, 5590–5599
23. Delcros, J.G., Tomasi, S., Duhieu, S., Foucault, M., Martin, B., Le Roch, M., Eifl er-Lima, V., Renault, J. and Uriac, P. (2006) Effect of polyamine homologation on the transport and biological proper-
ties of heterocyclic amidines. J. Med. Chem. 49, 232–245
24. Bolden, J.E., Peart, M.J. and Johnstone, R.W. (2006) Anticancer activities of histone deacetylase inhibitors. Nat. Rev. Drug Discov. 5, 769–784
25. Varghese, S., Gupta, D., Baran, T., Jiemjit, A., Gore, S.D., Casero, Jr, R.A. and Woster, P.M. (2005) Alkyl-substituted polyaminohydroxamic acids: a novel class of targeted histone deacetylase inhibi-
tors. J. Med. Chem. 48, 6350–6365
26. Varghese, S., Senanayake, T., Murray-Stewart, T., Doering, K., Fraser, A., Casero, Jr, R.A. and Woster, P.M. (2008) Polyaminohydroxamic acids and polyaminobenzamides as isoform selective
histone deacetylase inhibitors. J. Med. Chem. 51, 2447–2456
27. Lee, M., Wynder, C., Schmidt, D., McCafferty, D. and Shiekhattar, R. (2006) Histone H3 lysine 4 demethylation is a target of nonselective antidepressive medications. Chem. Biol. 13,
563–567
28. Binda, C., Mattevi, A. and Edmondson, D.E. (2002) Structure–function relationships in fl avoenzyme-dependent amine oxidations: a comparison of polyamine oxidase and monoamine
oxidase. J. Biol. Chem. 277, 23973–23976
29. Wang, J., Hevi, S., Kurash, J.K., Lei, H., Gay, F., Bajko, J., Su, H., Sun, W., Chang, H., Xu, G. et al. (2009) The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA meth-
ylation. Nat. Genet. 41, 125–129
30. Baylin, S.B. and Ohm, J.E. (2006) Epigenetic gene silencing in cancer: a mechanism for early onco- genic pathway addiction? Nat. Rev. Cancer 6, 107–116
31. Kahl, P., Gullotti, L., Heukamp, L.C., Wolf, S., Friedrichs, N., Vorreuther, R., Solleder, G., Bastian, P.J., Ellinger, J., Metzger, E. et al. (2006) Androgen receptor coactivators lysine-specifi c histone
demethylase 1 and four and a half LIM domain protein 2 predict risk of prostate cancer recur-
rence. Cancer Res. 66, 11341–11347
32. Scoumanne, A. and Chen, X. (2007) The lysine-specifi c demethylase 1 is required for cell prolif- eration in both p53-dependent and -independent manners. J. Biol. Chem. 282, 15471–15475
33. Bradley, C., van der Meer, R., Roodi, N., Yan, H., Chandrasekharan, M.B., Sun, Z.W., Mernaugh, R.L. and Parl, F.F. (2007) Carcinogen-induced histone alteration in normal human mammary
epithelial cells. Carcinogenesis 28, 2184–2192
34. Schulte, J.H., Lim, S., Schramm, A., Friedrichs, N., Koster, J., Versteeg, R., Ora, I., Pajtler, K., Klein-Hitpass, L., Kuhfi ttig-Kulle, S. et al. (2009) Lysine-specifi c demethylase 1 is strongly
expressed in poorly differentiated neuroblastoma: implications for therapy. Cancer Res. 69,
2065–2071
The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 109 10/9/09 4:38:47 PM Essays in Biochemistry volume 46 2009 35. Wang, Y., Hacker, A., Murray-Stewart, T., Frydman, B., Valasinas, A., Fraser, A.V., Woster, P.M. and Casero, Jr, R.A. (2005) Properties of recombinant human N1-acetylpolyamine oxidase
(hPAO): potential role in determining drug sensitivity. Cancer Chemother. Pharmacol. 56, 83–90
36. Huang, Y., Greene, E., Murray-Stewart, T., Goodwin, A., Baylin, S., Woster, P. and Casero, Jr, R. (2007) Inhibition of lysine-specifi c demethylase 1 by polyamine analogues results in reexpression
of aberrantly silenced genes. Proc. Natl. Acad. Sci. U.S.A. 104, 8023–8028
37. Stavropoulos, P. and Hoelz, A. (2007) Lysine-specifi c demethylase 1 as a potential therapeutic target. Expert Opin. Ther. Targets 11, 809–820
38. Huang, Y., Murray Stewart, T., Wu, Y., Marton, L., Woster, P. and Casero, R. (2009) Novel oligoamine/polyamine analogues inhibit lysine-specifi c demethylase 1 (LSD1), induce re-expression of epigenetically silenced genes, and inhibit the growth of established human tumors in vivo. AACR 100th Annual Meeting, Denver, CO, U.S.A., 18–22 April 2009, Abstract LB-173 39. Murray-Stewart, T., Huang, Y., Woster, P. and Casero, R. (2008) Polyamine analogue inhibition of lysine-specifi c demethylase 1 in human acute myeloid leukemia cell lines. Proc. Am. Assoc. Cancer
Res. 49, 2605
40. McGarvey, K., Fahrner, J., Greene, E., Martens, J., Jenuwein, T. and Baylin, S. (2006) Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic
chromatin state. Cancer Res. 66, 3541–3549
41. Pruitt, K., Zinn, R.L., Ohm, J.E., McGarvey, K.M., Kang, S.H., Watkins, D.N., Herman, J.G. and Baylin, S.B. (2006) Inhibition of SIRT1 reactivates silenced cancer genes without loss of promoter
DNA hypermethylation. PLoS Genet. 2, e40
42. Cameron, E., Bachman, K., Myohanen, S., Herman, J. and Baylin, S. (1999) Synergy of demethyla- tion and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat.
Genet. 21, 103–107
43. Gore, S.D., Baylin, S., Sugar, E., Carraway, H., Miller, C.B., Carducci, M., Grever, M., Galm, O., Dauses, T., Karp, J.E. et al. (2006) Combined DNA methyltransferase and histone deacetylase
inhibition in the treatment of myeloid neoplasms. Cancer Res. 66, 6361–6369
The Authors Journal compilation 2009 Biochemical Society 0046-0007 Casero.indd 110 10/9/09 4:38:48 PM

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