# Patent

## Title
Histone demethylation mediated by the nuclear amine oxidase homolog LSD1

## Abstract

LSD1, a homolog of nuclear amine oxidases, functions as a histone demethylase and transcriptional co-repressor. LSD1 specifically demethylates histone H3 lysine 4, which is linked to active transcription. Lysine demethylation occurs via an oxidation reaction that generates formaldehyde. Importantly, RNAi inhibition of LSD1 causes an increase in H3 lysine 4 methylation and concomitant de-repression of target genes, suggesting that LSD1 represses transcription via histone demethylation. The results thus identify a histone demethylase conserved from S. pombe to human and reveal dynamic regulation of histone methylation by both histone methylases and demethylases.

## Background
RELATED APPLICATIONS
This application is a divisional of U.S. application Ser. No. 11/721,789, filed on Feb. 19, 2009, issued as U.S. Pat. No. 7,741,086 on Jun. 22, 2010, which is a National Stage of International Application No, PCT/US05/045987, filed Dec. 16, 2005, which claims the benefit of U.S. Provisional Application No. 60/636,095, filed Dec. 16, 2004, each of which is specifically incorporated by reference herein.


GOVERNMENT INTEREST
This invention was made using funds from grant GM071004 from the U.S. National Institutes of Health. The U.S. government therefore retains certain rights in the invention.


TECHNICAL FIELD OF THE INVENTION
This invention is related to the area of gene regulation. In particular, it relates to the area of modification of chromosome structure as a means of regulating transcription. This modification importantly impacts disease processes as well as normal physiology and development.
BACKGROUND OF THE INVENTION
The histone N-terminal tails are subjected to multiple covalent modifications that affect chromatin structure and consequently transcription. One of the best-characterized modifications is acetylation, which is controlled by both histone acetyltransferases (HATs) and deacetylases (HDACs) suggesting that acetylation regulation is a dynamic process (Kouzarides, 2000). More recently, histone methylation has also emerged as a form of posttranslational modification that significantly impacts chromatin structure (Rice and Allis, 2001; Zhang and Reinberg, 2001). Unlike histone acetylation, which takes places only on lysine (K), methylation occurs on both lysine and arginine (R). While acetylation is generally correlated with active transcription (Roth et al., 2001), histone methylation is linked to both transcriptional activation and repression (Zhang and Reinberg, 2001). For instance, histone H3 K9 (H3-K9) methylation is associated with heterochromatin formation (Nakayama et al., 2001; Peters et al., 2002; Rea et al., 2000) and also euchromatic gene repression (Nielsen et al., 2001; Shi et al., 2003). In the case of heterochromatin assembly, H3-K9 is first methylated by Suv39H, and the methylated K9 is then recognized and bound by the chromodomain protein HP1 (Bannister et al., 2001; Lachner et al., 2001; Nakayama et al., 2001). The Suv39H-HP1 methylation system is proposed to be responsible for heterochromatin propagation. In contrast, methylation of histone H3 K4 (H3-K4) is linked to active transcription (Liang et al., 2004; Litt et al., 2001; Noma et al., 2001; Santos-Rosa et al., 2002; Schneider et al., 2004), as is methylation of arginine residues of histone H3 and H4 (Zhang and Reinberg, 2001). Mechanisms that underlie methylation-dependent transcriptional activation are not completely understood, although H3-K4-specific methylases have recently been shown to associate with RNA polymerase II (Hamamoto et al., 2004; Ng et al., 2003b).
While histone acetylation is dynamically regulated by HATs and HDACs, histone methylation has been considered a “permanent” modification. At least two models are currently being considered to explain the turnover of methyl groups on histones. The first one suggests that a cell may remove histone methylation by clipping the histone tail (Allis et al., 1980) or by replacing the methylated histone with a variant histone in the case of methyl group turnover at H3-K9 (Ahmad and Henikoff, 2002; Briggs et al., 2001; Johnson et al., 2004). However, this mechanism would not allow for dynamic regulation of histone methylation and the plasticity that may be essential for gene transcription regulation in some biological processes. The second model proposes the existence of histone demethylases that function to remove the methyl groups from lysine and arginine, which would make dynamic regulation possible. Recently, a human peptidyl arginine deiminase, PAD14/PAD4, has been shown to antagonize methylation on the arginine residues by converting arginine to citrulline, (Cuthbert et al., 2004; Wang et al., 2004). PAD14/PAD4 catalyzes the deimination reaction irrespective of whether the arginine residue is methylated or not. These findings suggest that histone methylation can be dynamically regulated through the opposing actions of histone methylases and enzymes such as PAD14/PAD4. However, since PAD14/PAD4 catalyzes deimination but not demethylation, it remains unclear whether bona fide histone demethylases exist. The search for histone demethylases began in the 1960s when Paik and colleagues first reported an enzyme that can demethylate free mono- and di-N-methyllysine (Kim et al., 1964). Subsequently, the same investigators partially purified an activity that can demethylate histones (Paik and Kim, 1973; Paik and Kim, 1974). These early studies suggested the possibility that histone demethylases may exist but the molecular identity of these putative histone demethylases have remained elusive for the past four decades.
Classical amine oxidases play important roles in metabolism and their substrates range from small molecules (e.g., spermine and spermidine) to proteins. More recently, amine oxidases have also been proposed to function as histone demethylases via an oxidation reaction that removes methyl groups from lysine or arginine residues of histones (Bannister et al., 2002). KIAA0601 encodes a protein that shares significant sequence homology with FAD-dependent amine oxidases (Humphrey et al., 2001; Shi et al., 2003). We identified KIAA0601/NPAO as a component of the CtBP co-repressor complex (Shi et al., 2003), and it has also been found in a number of other co-repressor complexes, including NRD (Tong et al., 1998), Co-REST (You et al., 2001), and subsets of the HDAC complexes (Hakimi et al., 2002; Hakimi et al., 2003; Humphrey et al., 2001). Recent studies of the C. elegans homolog, SPR-5, provided genetic evidence for a role in transcriptional repression (Eimer et al., 2003; Jarriault and Greenwald, 2002). However, its exact role in transcriptional regulation has been unclear.
There is a continuing need in the art to identify the components of the transcription regulatory system so that they can be manipulated to treat diseases that involve aberrations of the system.
SUMMARY OF THE INVENTION
In one embodiment of the invention a method is provided for monitoring eukaryotic histone demethylase activity. An eukaryotic histone demethylase protein is contacted with a histone peptide. The histone peptide is lysine- or arginine-methylated. The methylation status of the histone peptide is determined.
A second embodiment of the invention provides a method of screening for modulators of eukaryotic histone demethylase activity. An eukaryotic histone demethylase protein and a histone peptide are contacted in the presence and in the absence of a test substance. The histone peptide is lysine-methylated. The methylation status of the histone peptide is determined A test substance is identified as an inhibitor of eukaryotic histone demethylase activity if more methylated lysine is found in the presence than in the absence of the test substance. A test substance is identified as an enhancer of eukaryotic histone demethylase protein activity if less methylated lysine is found in the presence than in the absence of the test substance.
A third embodiment of the invention provides a method of up-regulating methylated histone-activated genes. An RNAi for an eukaryotic histone demethylase is administered to cells in an amount sufficient to inhibit expression of the eukaryotic histone demethylase.
A fourth embodiment of the invention provides a method of up-regulating methylated histone-activated genes. An antisense RNA for an eukaryotic histone demethylase is administered to cells in an amount sufficient to inhibit expression of the eukaryotic histone demethylase.
A fifth embodiment of the invention provides a method of up-regulating methylated histone-activated genes. An antisense construct for an eukaryotic histone demethylase is administered to cells in an amount sufficient to inhibit expression of the eukaryotic histone demethylase.
A sixth embodiment of the invention provides a method of down-regulating methylated histone-activated genes. An expression vector encoding an eukaryotic histone demethylase is administered to cells in an amount sufficient to increase expression of the eukaryotic histone demethylase in the cell.
A seventh embodiment of the invention provides a method of screening for modulators of LSD1 activity. A LSD1 protein and a histone peptide are contacted in the presence and in the absence of a test substance. The histone peptide comprises at least six contiguous amino acid residues of histone H3 which include lysine residue 4, and the lysine residue 4 is mono- or di-methylated. The methylation status of the histone peptide is determined A test substance is identified as an inhibitor of LSD1 activity if more methylated lysine is found in the presence than in the absence of the test substance. A test substance is identified as an enhancer of LSD1 activity if less methylated lysine residue 4 is found in the presence than in the absence of the test substance.
An eighth embodiment of the invention provides a method of up-regulating methyl lysine 4 histone 3-activated genes. An RNAi for LSD1 is administered to cells in an amount sufficient to inhibit expression of the LSD1 histone demethylase.
A ninth embodiment of the invention provides a method of up-regulating methyl lysine 4 histone 3-activated genes. An antisense RNA for LSD1 histone demethylase is administered to cells in an amount sufficient to inhibit expression of the LSD1 histone demethylase.
A tenth embodiment of the invention provides a method of up-regulating methyl lysine 4 histone 3-activated genes. An antisense construct for an LSD1 histone demethylase is administered to cells in an amount sufficient to inhibit expression of the LSD1 histone demethylase.
An eleventh embodiment of the invention provides a method of down-regulating methyl lysine 4 histone 3-activated genes. An expression vector encoding LSD1 histone demethylase is administered to cells in an amount sufficient to increase expression of the eukaryotic histone demethylase in the cell.
A twelfth embodiment of the invention provides a method of up-regulating methylated histone-repressed genes. An inhibitor for an eukaryotic histone demethylase is administered to cells in an amount sufficient to inhibit activity of the eukaryotic histone demethylase.
A thirteenth embodiment of the invention provides a method of down-regulating methylated histone-activated genes. An enhancer of an eukaryotic histone demethylase is administered to cells in an amount sufficient to increase activity of the eukaryotic histone demethylase. Other embodiments are further described in the claims and specification.
Also provided herein are methods for identifying an agent that modulates the interaction between a histone demethylase protein and a CoREST protein. A method may comprise contacting a histone demethylase reagent and a CoREST reagent in the presence of a test agent; and (ii) determining the level of interaction between the histone demethylase reagent and the CoREST reagent, wherein a different level of interaction between the histone demethylase reagent and the CoREST reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the interaction between a histone demethylase protein and a CoREST protein. A method may further comprise at least one other component of a histone demethylase transcription complex. A method may further comprise determining the effect of the test agent on a biological activity of the histone demethylase, e.g., by a method comprising contacting a histone demethylase reagent and a CoREST reagent with the test agent and determining the biological activity of the histone demethylase reagent, wherein a different activity of the histone demethylase reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the biological activity of a histone demethylase.
Further provided are methods for identifying an agent that modulates the biological activity of a histone demethylase. A method may comprise (i) contacting a histone demethylase reagent with a CoREST reagent in the presence of a test agent; and (ii) determining the biological activity of the histone demethylase reagent, wherein a different activity of the histone demethylase reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the biological activity of a histone demethylase. The biological activity of the histone demethylase reagent is demethylase activity or amine oxidase activity. The CoREST reagent may comprise at least about amino acids 293 to 381 at least about amino acids 293 to 482 of human CoREST.
A method for identifying an agent that modulates the interaction between a histone demethylase protein and a BHC80 protein may comprise contacting a histone demethylase reagent and a BHC80 reagent in the presence of a test agent; and (ii) determining the level of interaction between the histone demethylase reagent and the BHC80 reagent, wherein a different level of interaction between the histone demethylase reagent and the BHC80 reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the interaction between a histone demethylase protein and a BHC80 protein. A method may further comprise at least one other component of a histone demethylase transcription complex. A method may further comprise determining the effect of the test agent on a biological activity of the histone demethylase, e.g., by a method comprising contacting a histone demethylase reagent and a HDC80 reagent with the test agent and determining the biological activity of the histone demethylase reagent, wherein a different activity of the histone demethylase reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the biological activity of a histone demethylase.
A method for identifying an agent that modulates the biological activity of a histone demethylase may comprise (i) contacting a histone demethylase reagent with a HDC80 reagent in the presence of a test agent; and (ii) determining the biological activity of the histone demethylase reagent, wherein a different activity of the histone demethylase reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the biological activity of a histone demethylase. The biological activity of the histone demethylase reagent may be demethylase activity or amine oxidase activity.
Also provided herein are molecular complexes or compositions, e.g., pharmaceutical compositions, comprising a histone demethylase reagent and a CoREST reagent; and/or a BHC80 reagent.
A method for repressing the transcription of a methylated histone activated gene in a cell may comprise contacting the cell with, or administering into the cell, an agent that increases the protein or activity level of a histone demethylase in the cell. The agent may be a histone demethylase protein or functional homolog thereof The agent may also be a nucleic acid encoding a histone demethylase protein or functional homolog thereof The agent may be an agent that increases the level of protein or activity of CoREST. The agent may be a CoREST protein or functional homolog thereof The agent may be a nucleic acid encoding a CoREST protein or functional homolog thereof The agent may be an agent that stimulates the interaction between a histone demethylase and CoREST. The agent may be an agent that decreases the level of protein or activity of BHC80, e.g., a BHC80 siRNA, or an agent that inhibits the interaction between a histone demethylase and BHC80. The method may further comprise contacting the cell with, or administering into the cell, a second agent that increases the level or protein or activity of a histone deacetylase (HDAC). The second agent may be an HDAC protein or a functional homolog thereof The second agent may be a nucleic acid encoding an HDAC protein or a functional homolog thereof.
Other exemplary methods provided herein include methods for increasing the transcription of a methylated histone activated gene in a cell, comprising contacting the cell with an agent that decreases the protein or activity level of a histone demethylase in the cell. The agent may be a histone demethylase siRNA; an agent that decreases the protein or activity level of CoREST in the cell, such as a CoREST siRNA; an agent that inhibits the interaction between a histone demethylase and CoREST; an agent that increases the level of protein or activity of BHC80, such as a BHC80 protein or functional homolog thereof or a nucleic acid encoding a BHC80 protein or functional homolog thereof; or an agent that stimulates the interaction between a histone demethylase and BHC80. A method may further comprise contacting the cell with, or administering into the cell, a second agent that decreases the level or activity of an HDAC.
A method for treating or preventing a disease associated with the abnormal expression of a methylated histone activated gene in a subject may comprise administering to the subject a therapeutically effective amount of an agent that modulates the level of protein or activity of a histone demethylase. The disease may be a hyperproliferative disease, e.g. cancer, and the agent is an agent that increases the level of protein or activity of a histone demethylase. The method may further comprise administering to the subject a therapeutically effective amount of a second agent that increases the level of protein or activity of a histone deacetylase. The first and second agents may be administered to the subject by intratumoral injection, perfusion of a target tissue through its vasculature or by direct injection to a target tissue.
These and other embodiments which will be apparent to those of skill in the art upon reading the specification provide the art with reagents and methods for drug screening and therapy relating to histone methylation, neurological diseases and cancer.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A-1C. LSD1 is a transcriptional co-repressor and is evolutionarily conserved. FIG. 1A. Diagram of the LSD1-like amine oxidase family members in different species. The deduced amino acid sequences are retrieved from NCBI GenBank and analyzed by the NCBI Conserved Domain Search Program. The SWIRM, amine oxidase domains and FAD binding motif are drawn proportionally. Some family members contain a spacer region in their amine oxidase domain, which is shown by white-red stripes. Additionally, the S. pombe protein SPAC23E2.02 contains a HMG domain and A. thaliana protein AAF19542 has an EFh and a copper amine oxidase domain. FIG. 1B. Two subfamilies of LSD1-like proteins. The amine oxidase domains of these proteins are classified into two subfamilies based on ClustalW-aligned phylogenetic tree. A noted difference is that the LSD1 subfamily (7 members) contains the spacer region but not the AOF1 subfamily (6 members) (except NP—193364.1). FIG. 1C. Diagrams of G4LSD1 and the C-terminal deletion mutant G4LSD1ΔC. AO: amine oxidase.
FIG. 2. Demethylation of diMeK4H3 peptides by LSD1. Possible chemical reactions for LSD1-catalyzed demethylation. Only diMeK4H3 is shown, but the proposed reactions are also compatible with mono-methylated lysines or methylated arginines.
FIG. 3 shows diagrams of CoREST deletion mutants.



DETAILED DESCRIPTION OF THE INVENTION
It is a discovery of the present inventors that LSD1 functions as a transcriptional co-repressor that participates in the silencing of endogenous neuron-specific genes. Significantly, RNAi knock down of LSD1 results in an increase in histone H3-K4 methylation and a concomitant de-repression of the target genes. These findings indicate that LSD1 represses transcription by demethylating histone H3 at K4, whose methylation is linked to active transcription (Liang et al., 2004; Litt et al., 2001; Noma et al., 2001; Santos-Rosa et al., 2002; Schneider et al., 2004). Since LSD1 and its related proteins are present from S. pombe to mammals, demethylation is likely an evolutionarily conserved function for this family of proteins. The identification of LSD1 as a histone demethylase indicates that histone methylation, like histone acetylation, is a dynamic process and is subject to regulation by both methylases and demethylases.
It has also been shown herein that the activity of LSD1 is modulated by its interaction with other proteins, such as CoREST and BHC80, as well as by the acetylation status of histones that are bound to the promoter of LSD1 target genes.
Exemplary Methods and Composition
Provided herein are methods for modulating the expression of genes that are regulated by methylation/demethylation of a transcriptional regulator protein, such as a histone (“demethylase target gene”). Some genes are upregulated by methylation of a histone (“methylated histone-activated genes”), whereas other genes are downregulated by methylation of a histone (“methylated histone-repressed gene”). The following genes are upregulated by the methylation of histone H3 at the lysine K4: M4 AchR, SCN1A, SCN2A, SCN3A, and p57. Other target genes include those containing a REST-respsonsive repressor element 1 (RE1). These genes are repressed by a demethylase, such as LSD1. Accordingly, the expression of these methylated histone-activated genes can be repressed by the presence of LSD1 and activated (or derepressed) by removing LSD1, such as by using an LSD1 siRNA or antisense or dominant negative mutant. Similarly, methylated histone-activated genes can be represssed by the presence of CoREST and activated (or derepressed) by removing CoREST, such as by using a CoREST siRNA or antisense or dominant negative mutant. In addition, methylated histone-activated genes can be represssed by removing BHC80, such as by using a BHC80 siRNA or antisense or dominant negative mutant, and activated by the presence of BHC80. The methylated histone-activated genes may also be modulated by modulating the expression of one or more of LSD1, CoREST and BHC80.
Genes that are downregulated by the methylation of histone H3 include those that are regulated by the androgen receptor (Metzger et al. (2005) Nature 437:436), such as those containing an androgen receptor element (ARE) in their promoter. Exemplary genes that are regulated by the androgen receptor include: prostate specific antigen isoform 1 (PSA)(NP—001639); Synaptotagmin-like 4 (SYTL4) (CAI42004); nerve growth factor receptor associated protein 1(NGFRAP1) (CAI41523); 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (PFKFB1) (NP—002616); fatty acid synthase (FAS) (NP—004095); and Proteinase-activated receptor 1 precursor (PAR-1) (P25116). Genes regulated by the androgen receptor may be activated by a demethylase, such as LSD1. Accordingly, the expression of these methylated histone-repressed genes can be activated (or derepressed) by the presence of LSD1 and repressed by removing LSD1, such as by using an LSD1 siRNA or antisense or dominant negative mutant. Expression of methylated histone-repressed genes can also be activated (or derepressed) by the presence of CoREST and repressed by removing CoREST, such as by using a CoREST siRNA or antisense or dominant negative mutant. In addition, methylated histone-repressed genes can be activated by removing BHC80, such as by using a BHC80 siRNA or antisense or dominant negative mutant, and repressed by the presence of BHC80. The methylated histone-repressed genes may also be modulated by modulating the expression of one or more of LSD1, CoREST and BHC80.
The following Table I summarizes how gene expression of methylated histone-repressed and histone-activated genes can be modulated:














Gene
modulation
LSD1
CoREST
BHC80







methylated
activation
increase
increase
decrease


histone-repressed
repression
decrease
decrease
increase


methylated
activation
decrease
decrease
increase


histone-activated
repression
increase
increase
decrease









In Table I, “increase” of a protein refers to increasing its level of protein or activity. Increasing the level of protein or activity of a particular protein in a cell may be achieved by contacting the cell with, or administering into the cell: the protein or a functional homolog thereof; a nucleic acid (e.g., an expression vector) encoding the protein or a functional homolog thereof; an agent that upregulates the level of expression of the gene encoding the protein; or an agent that upregulates the activity of the protein, such as a cofactor. Increasing the level of protein or activity of a protein may be by a factor of at least about 50%, 2 fold, 5 fold, 10 fold, 30 fold, 50 fold or 100 fold.
In Table I, “decrease” of a protein refers to decreasing its level of protein or activity. Decreasing the level of protein or activity of a particular protein in a cell may be achieved by contacting the cell with, or administering into the cell: an siRNA; an antisense; a ribozyme; a triplex nucleic acid; a dominant negative mutant of the protein; a substrate mimetic; an agent that down-regulates the expression of the gene encoding the protein; or an agent that decreases the activity of the protein. Decreasing the level of protein or activity of a protein may be by a factor of at least about 50%, 2 fold, 5 fold, 10 fold, 30 fold, 50 fold or 100 fold.
Eukaryotic histone demethylase enzymes, according to the present invention are those eukaryotic proteins which have a SWIRM domain, a FAD binding motif, and an amine oxidase domain. The presence of these domains can be determined using tools available in the art including NCBI GenBank and NCBI Conserved Domain Search Program. Particular exemplary members of this class of enzymes are shown in FIG. 1A.
A histone demethylase may be an enzyme that demethylates the residue K4 on histone H3 (a “H3-K4 demethylase”). An exemplary H3-K4 demethylase is LSD1, which is also referred to as “FAD-binding protein BRAF35-HDAC complex, 110 kDa subunit” (“BHC110”), “KIAA0601”, and “amine oxidase (flavin containing) domain 2” (“AOF2”). The protein exists in two isoforms: variant (1) represents the longer transcript and encodes the longer isoform (a); and variant (2) lacks two alternate in-frame exons, compared to variant 1, resulting in a shorter protein (isoform b), compared to isoform a.
The following Table (Table 2) provides references for the nucleotide and amino acid sequences of the human LSD1 proteins:
















SEQ

SEQ


isoform
nucleic acid
ID NO
protein
ID NO







a
NM_015013.2
28
NP_001009999 (876 aas)
29


b
NM_015013.2
30
NP_055828.2 (852 aas)
31
















TABLE 3







Approximate location of conserved domains in human LSD1 proteins:










isoform
amino oxidase domain
SWIRM domain
FAD binding motif





a
aas 548-849; 311-450
aas 195-284
aas 300-359


b
aas 524-825; 291-426
aas 175-264
aas 280-339









The amino acid sequence of the FAD binding motif is







(SEQ ID NO: 43)


KVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADL


GAMVVTGLGG.






Another demethylase is AOF1 or amine oxidase (flavin containing) domain 1 protein. The amino acid and nucleotide sequences of human AOF1 are set forth in GenBank Accession numbers NM—153042 (SEQ ID NO: 36) and NP—694587 (SEQ ID NO: 37) and in SEQ ID NOs: 26 and 27, respectively. An NAD/FAD-dependent oxidoreductase domain is located at about amino acids 268-588 and a flaying containing amine oxidoreductase domain located at about amino acids 319-587 and 267-322 of SEQ ID NO: 37.
“CoREST” is a corepressor of RE1-silencing transcription factor (REST) and is also referred to as “REST corepressor 1” and “RCOR1”. The nucleotide and amino acid sequences of human CoREST are set forth in GenBank Accession Nos. NM—015156.1 and NP—055971.1 (482 amino acids), which correspond to SEQ ID NOs: 32 and 33, respectively. The human protein contains the following conserved domains: SANT1 (about amino acids 190-293), SANT2 (about amino acids 381-450) and ELM (about amino acids 105-182).
“BHC80” is also referred to as “PHD finger protein 21A” (“PHF21A”), “BM-006” and “KIAA1696,” and is a component of the “BRAF35/HDAC2 complex” or “BRAF35/HDAC2 complex (80 kDa).” The nucleotide and amino acid sequences of the human BHC80 are set forth in GenBank Accession Nos. NM—016621.2 and NP—057705.2, which correspond to SEQ ID NOs: 34 and 35, respectively. The human protein contains a PHD zinc finger domain at about amino acids 444-487.
BHC is a multiprotein complex consisting of two enzymatic activities: a histone deacetylase (HDAC1 or 2) and LSD1.
Human histone H3 is encoded by the nucleotide sequence set forth in GenBank Accession No. NM—003493.2 and has the amino acid sequence set forth in GenBank Accession No. NP—003484.1.
A homolog of a protein of interest, such as LSD1, CoREST or BHC80, includes proteins comprising or consisting of an amino acid sequence that has at least about 70%, 80%, 90%, 95%, 98% or 99% identity with the amino acid sequence of the protein described herein, such as SEQ ID NOs: 23, 26, 29, 31, 33, 35 and 37. A homolog may also be a protein that is encoded by a nucleic acid that has at least about 70%, 80%, 90%, 95%, 98% or 99% identity with a nucleotide sequence described herein, such as SEQ ID NOs: 24, 27, 28, 30, 32, 34 and 36 or the coding sequence thereof A homolog may also be a protein that is encoded by a nucleic acid that hybridizes, e.g., under stringent hybridization conditions, to a nucleic acid consisting of a nucleotide sequence described herein, e.g., SEQ ID NOs: 24, 27, 28, 30, 32, 34 and 36, or the coding sequence thereof.
For example, homologs may be encoded by nucleic acids that hybridize under high stringency conditions of 0.2 to 1×SSC at 65° C. followed by a wash at 0.2×SSC at 65° C. to a nucleic acid consisting of a sequence described herein. Nucleic acids that hybridize under low stringency conditions of 6×SSC at room temperature followed by a wash at 2×SSC at room temperature to nucleic acid consisting of a sequence described herein or a portion thereof can be used. Other hybridization conditions include 3×SSC at 40 or 50° C., followed by a wash in 1 or 2×SSC at 20, 30, 40, 50, 60, or 65° C. Hybridizations can be conducted in the presence of formaldehyde, e.g., 10%, 20%, 30% 40% or 50%, which further increases the stringency of hybridization. Theory and practice of nucleic acid hybridization is described, e.g., in S. Agrawal (ed.) Methods in Molecular Biology, volume 20; and Tijssen (1993) Laboratory Techniques in biochemistry and molecular biology-hybridization with nucleic acid probes, e.g., part I chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays,” Elsevier, New York provide a basic guide to nucleic acid hybridization.
Homologs of proteins described herein, such as LSD1, CoREST and BHC80 may also be analogs, e.g., that differ from the naturally occurring protein, e.g. a protein having an amino acid sequence set forth as SEQ ID NO: 23, 26, 29, 31, 33, 35 and 37, by conservative amino acid sequence differences or by modifications which do not affect sequence, or by both. Analogs can differ from naturally occurring proteins by conservative amino acid sequence differences or by modifications which do not affect sequence, or by both. Any number of procedures may be used for the generation of mutant, derivative or variant forms of a protein of interest using recombinant DNA methodology well known in the art such as, for example, that described in Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York) and Ausubel et al. (1997, Current Protocols in Molecular Biology, Green & Wiley, New York).
For example, conservative amino acid changes may be made, which although they alter the primary sequence of the protein or peptide, do not normally alter its function. Conservative amino acid substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine (in positions other than proteolytic enzyme recognition sites); phenylalanine, tyrosine.
Homologs of a protein of interest also includes portions thereof, such as portions comprising one or more conserved domains, such as those described herein.
A “functional homolog” of a protein of interest refers to a homolog of the protein having at least one biological activity of the protein. For example, a functional homolog of LSD1 may be a protein having an amine oxidase activity, a demethylase activity, the ability to bind to another protein, such as CoREST or BHC80 or a protein from a nucleosome, or other biological activities, such as those described herein.
A functional homolog of LSD1 may be a portion of the wild type LSD1 protein including one or more of the conserved domains. A functional homolog of LSD1 may comprise at least a portion of the amino oxidase domain, the SWIRM domain and/or the FAD binding motif Exemplary functional homologs of LSD1 isoform a include polypeptides comprising from about amino acid 195, 190, 175, 150 or 100 to about amino acid 849, 850, 860, 870 or 876 of SEQ ID NO: 29. Exemplary functional homologs of LSD1 isoform b include polypeptides comprising from about amino acid 175, 174, 170, 150 or 100 to about amino acid 825, 830, 840, 850, 851 or 852 of SEQ ID NO: 31. Functional LSD1 homologs may also include those comprising an amino acid sequence from about amino acid 311, 310, 300 or 250 to about amino acid 849, 850, 860, 870 or 876 of SEQ ID NO: 29 (LSD1 isoform a) and those comprising an amino acid sequence from about amino acid 291, 290, 280, 270 or 250 to about amino acid 825, 830, 840, 850, 851 or 852 of SEQ ID NO: 31 (homologs comprising the amino oxidase domain). Other LSD1 homologs that may have a biological activity include those comprising the SWIRM domain, e.g., about amino acid 195, 190, 175, 150 or 100 to about amino acid 284, 285, 290 or 300 of SEQ ID NO: 29 (LSD1 isoform a) or about amino acid 175, 174, 170, 150 or 100 to about amino acid 264, 265, 270, 280, 290 or 300 of SEQ ID NO: 31 (LSD1 isoform b).
Functional homologs of AOF1 include an oxidoreductase domain, e.g., the NAD/FAD-dependent oxidoreductase domain or the flavin containing amine oxidoreductase domain. Exemplary functional homologs of AOF1 include those comprising from about amino acid 268, 260, 250 or 200 to about amino acid 588, 590, 595 or 600 of SEQ ID NO: 37.
Functional homologs of CoREST include the ELM, SANT1 and/or SANT2 domains. Exemplary functional homologs of CoREST include those comprising about from about amino acid 293, 290, 280, 270, 260 or 250 to about amino acid 480 or 482 of SEQ ID NO: 33. Other CoREST functional homologs may comprise from about amino acid 293, 290, 280, 270, 260 or 250 to about amino acid 381, 385, 390 or 300 of SEQ ID NO: 31.
Functional homologs of BHC80 comprise at least about amino acid 444, 440, 430, or 400 to about amino acid 487, 490, or 500 of SEQ ID NO: 35.
Whether a homolog is a functional homolog can be determined according to methods known in the art. For example, a demethylase activity can be determined as described in the Examples. An illustrative example for determining whether a demethylase homolog has demethylase activity includes contacting the demethylase homolog with a target peptide that is methylated, and determining whether the demethylase homolog is capable of demethylating the target peptide. The assay may further comprise one or more other components, such as other proteins, e.g., CoREST, or cofactors, e.g., flavin adenine dinucleotide (FAD). A target peptide may be a histone peptide. Any histone peptide can be used. Preferably it is used with a histone demethylase enzyme that recognizes the histone peptide as a substrate. The full histone protein can be used or a peptide comprising only a portion of the histone protein can be used, so long as that portion contains the methylated residue upon which the demethylase enzyme acts and the portion contains sufficient contextual residues to permit its recognition by the enzyme. Typically at least 3, at least 4, at least 5, at least 6, or at least 7 residues on either side of the methylated residue are believed to be sufficient for recognition. The methylated residue can be either a lysine or an arginine. Preferably the histone peptide and the histone demethylase are derived from the same species of organism.
Measurement of the reaction between a histone and an eukaryotic histone demethylase protein can be accomplished by any means known in the art. These include, without limitation Western blotting, measuring formation of formaldehyde, mass spectrometry, and measuring formation of peroxide.
Methods for modulating the expression of a gene whose expression is modulated by the methylation status of one or more histones may comprise modulating the acetylation/deacetylation status of one or more histones. In one embodiment, demethylation is facilitated or improved by deacetylation. Accordingly, in certain embodiments, a method comprising increasing LSD1 protein level or activity in a cell comprises contacting the cell with an agent that increases histone deacetylase (HDAC) protein or activity levels and/or an agent that decreases histone acetylase protein or activity levels. On the other hand, a method comprising decreasing LSD1 protein level or activity in a cell may comprise contacting the cell with an agent that decreases HDAC protein or activity levels and/or an agent that increases histone acetylase protein or activity levels.
Methods for modulating the expression of a gene whose expression is modulated by the methylation status of one or more histones may also comprise (i) modulating the methylation status and (ii) modulating the acetylation status of one or more histones involved in regulating the expression of the gene.
The following Table (Table 4) summarizes how gene expression of methylated histone-repressed and histone-activated genes can be modulated by modulating the level of protein or activity of deacetylases or acetylases:













Gene
modulation
deacetylase
acetylase







methylated histone-repressed
activation
increase
decrease



repression
decrease
increase


methylated histone-activated
activation
decrease
increase



repression
increase
decrease









“Increase” and “decrease” is as described above for Table 1.
An “acetylase” is used interchangeable herein with “acetyl transferase” and refers to an enzyme that catalyzes the addition of an acetyl group (CH3CO−) to an amino acid. Exemplary acetyl transferases are histone acetyl transferases (HAT).
The term “deacetylase” refers to an enzyme that catalyzes the removal of an acetyl group (CH3CO−) from an amino acid. Class I histone deacetylases (HDACs) includes the yeast Rpd3-like proteins (HDAC1, HDAC2, HDAC3, HDAC8, and HDAC11. Class II HDACs includes the yeast Hda1-like proteins HDAC4, HDAC5, HDAC6, HDAC7, HDAC9, and HDAC10 (Fischle, W., et al., J. Biol. Chem, 274, 11713-11720 (1999)). Class III HDACs includes the silent mating type information regulation 2 (Sir2) and homologs thereof, such as SIRT1 in humans.
The nucleotide and amino acid sequences of each of these human HDACs and the location of conserved domains in their amino acid sequences is set forth in the following table (Table 5) (“i” refers to “isoform”):














nucleotide
amino acid 
conserved domains


HDAC
sequence
sequence
(in amino acids)



















HDAC1

NM_004964
NP_004955
28-321


HDAC2

NM_001527
NP_001518
29-322


HDAC3

NM_003883
NP_003874
 3-315


HDAC4

NM_006037
NP_006028
91-142; 653-994


HDAC5
i1
NM_001015053
NP_001015053
683-1026



i2
NM_005474
NP_005465
682-1025


HDAC6

NM_006044
NP_006035
1132-1180; 883-1068;






480-796; 84-404


HDAC7A
i1
NM_015401
NP_056216
519-829 



i2
NM_016596
NP_057680
479-789 


HDAC8

NM_018486
NP_060956
16-324


HDAC9
i1
NM_014707
NP_055522




i2
NM_058176
NP_478056
633-974 



i3
NM_058177
NP_478057
633-860 



i4
NM_178423
NP_848510
633-974 



i5
NM_178425
NP_848512
636-977 


HDAC10

NM_032019
NP_114408
 1-315


HDAC11

NM_024827
NP_079103
17-321


SIRT1

NM_012238
NP_036370
431-536; 254-489


SIRT2
i1
NM_012237
NP_036369
77-331



i2
NM_030593
NP_085096
40-294


SIRT3
ia
NM_012239
NP_036371
138-373 



ib
NM_001017524
NP_001017524
 1-231


SIRT4

NM_012240
NP_036372
47-308


SIRT5
i1
NM_012241
NP_036373
51-301



i2
NM_031244
NP_112534
51-287


SIRT6

NM_016539
NP_057623
45-257


SIRT7

NM_016538
NP_057622
100-314 









Other sirtuin family members include the yeast Sir2-like genes termed “HST genes” (homologues of Sir two) HST1, HST2, HST3 and HST4 and their human homologues.
Methods for modulating gene expression of methylated histone repressed or activated genes may also include modulating the level of protein or activity of methylases. Thus, in a situation in which one desires to reduce methylation, a method may comprise decreasing the level of protein or activity of one or more methylases, whereas in a situation in which one desires to increase methylation, a method may comprise increasing the level of protein or activity of one or more methylases.
Nucleic acids, e.g., those encoding a protein of interest or functional homolog thereof, or a nucleic acid intended to inhibit the production of a protein of interest (e.g., siRNA or antisense RNA) can be delivered to cells, e.g., eukaryotic cells, in culture, to cells ex vivo, and to cells in vivo. The cells can be of any type including without limitation cancer cells, stem cells, neuronal cells, and non-neuronal cells. The delivery of nucleic acids can be by any technique known in the art including viral mediated gene transfer, liposome mediated gene transfer, direct injection into a target tissue, organ, or tumor, injection into vasculature which supplies a target tissue or organ.
Polynucleotides can be administered in any suitable formulations known in the art. These can be as virus particles, as naked DNA, in liposomes, in complexes with polymeric carriers, etc. Polynucleotides can be administered to the arteries which feed a tissue or tumor. They can also be administered to adjacent tissue, whether tumor or normal, which could express the demethylase protein.
Nucleic acids can be delivered in any desired vector. These include viral or non-viral vectors, including adenovirus vectors, adeno-associated virus vectors, retrovirus vectors, lentivirus vectors, and plasmid vectors. Exemplary types of viruses include HSV (herpes simplex virus), AAV (adeno associated virus), HIV (human immunodeficiency virus), BIV (bovine immunodeficiency virus), and MLV (murine leukemia virus). Nucleic acids can be administered in any desired format that provides sufficiently efficient delivery levels, including in virus particles, in liposomes, in nanoparticles, and complexed to polymers.
The nucleic acids encoding a protein or nucleic acid of interest may be in a plasmid or viral vector, or other vector as is known in the art. Such vectors are well known and any can be selected for a particular application. In one embodiment of the invention, the gene delivery vehicle comprises a promoter and a demethylase coding sequence. Preferred promoters are tissue-specific promoters and promoters which are activated by cellular proliferation, such as the thymidine kinase and thymidylate synthase promoters. Other preferred promoters include promoters which are activatable by infection with a virus, such as the α- and β-interferon promoters, and promoters which are activatable by a hormone, such as estrogen. Other promoters which can be used include the Moloney virus LTR, the CMV promoter, and the mouse albumin promoter. A promoter may be constitutive or inducible.
In another embodiment, naked polynucleotide molecules are used as gene delivery vehicles, as described in WO 90/11092 and U.S. Pat. No. 5,580,859. Such gene delivery vehicles can be either growth factor DNA or RNA and, in certain embodiments, are linked to killed adenovirus. Curiel et al., Hum. Gene. Ther. 3:147-154, 1992. Other vehicles which can optionally be used include DNA-ligand (Wu et al., J. Biol. Chem. 264:16985-16987, 1989), lipid-DNA combinations (Felgner et al., Proc. Natl. Acad. Sci. USA 84:7413 7417, 1989), liposomes (Wang et al., Proc. Natl. Acad. Sci. 84:7851-7855, 1987) and microprojectiles (Williams et al., Proc. Natl. Acad. Sci. 88:2726-2730, 1991).
A gene delivery vehicle can optionally comprise viral sequences such as a viral origin of replication or packaging signal. These viral sequences can be selected from viruses such as astrovirus, coronavirus, orthomyxovirus, papovavirus, paramyxovirus, parvovirus, picornavirus, poxvirus, retrovirus, togavirus or adenovirus. In a preferred embodiment, the growth factor gene delivery vehicle is a recombinant retroviral vector. Recombinant retroviruses and various uses thereof have been described in numerous references including, for example, Mann et al., Cell 33:153, 1983, Cane and Mulligan, Proc. Nat'l. Acad. Sci. USA 81:6349, 1984, Miller et al., Human Gene Therapy 1:5-14, 1990, U.S. Pat. Nos. 4,405,712, 4,861,719, and 4,980,289, and PCT Application Nos. WO 89/02,468, WO 89/05,349, and WO 90/02,806. Numerous retroviral gene delivery vehicles can be utilized in the present invention, including for example those described in EP 0,415,731; WO 90/07936; WO 94/03622; WO 93/25698; WO 93/25234; U.S. Pat. No. 5,219,740; WO 9311230; WO 9310218; Vile and Hart, Cancer Res. 53:3860-3864, 1993; Vile and Hart, Cancer Res. 53:962-967, 1993; Ram et al., Cancer Res. 53:83-88, 1993; Takamiya et al., J. Neurosci. Res. 33:493-503, 1992; Baba et al., J. Neurosurg. 79:729-735, 1993 (U.S. Pat. No. 4,777,127, GB 2,200,651, EP 0,345,242 and WO91/02805).
A polynucleotide of interest can also be combined with a condensing agent to form a gene delivery vehicle. The condensing agent may be a polycation, such as polylysine, polyarginine, polyornithine, protamine, spermine, spermidine, and putrescine. Many suitable methods for making such linkages are known in the art.
In an alternative embodiment, a polynucleotide of interest is associated with a liposome to form a gene delivery vehicle. Liposomes are small, lipid vesicles comprised of an aqueous compartment enclosed by a lipid bilayer, typically spherical or slightly elongated structures several hundred Angstroms in diameter. Under appropriate conditions, a liposome can fuse with the plasma membrane of a cell or with the membrane of an endocytic vesicle within a cell which has internalized the liposome, thereby releasing its contents into the cytoplasm. Prior to interaction with the surface of a cell, however, the liposome membrane acts as a relatively impermeable barrier which sequesters and protects its contents, for example, from degradative enzymes. Additionally, because a liposome is a synthetic structure, specially designed liposomes can be produced which incorporate desirable features. See Stryer, Biochemistry, pp. 236-240, 1975 (W.H. Freeman, San Francisco, Calif.); Szoka et al., Biochim. Biophys. Acta 600:1, 1980; Bayer et al., Biochim. Biophys. Acta. 550:464, 1979; Rivnay et al., Meth. Enzymol. 149:119, 1987; Wang et al., PROC. NATL. ACAD. SCI. U.S.A. 84: 7851, 1987, Plant et al., Anal. Biochem. 176:420, 1989, and U.S. Pat. No. 4,762,915. Liposomes can encapsulate a variety of nucleic acid molecules including DNA, RNA, plasmids, and expression constructs comprising growth factor polynucleotides such those disclosed in the present invention.
Liposomal preparations for use in the present invention include cationic (positively charged), anionic (negatively charged) and neutral preparations. Cationic liposomes have been shown to mediate intracellular delivery of plasmid DNA (Felgner et al., Proc. Natl. Acad. Sci. USA 84:7413-7416, 1987), mRNA (Malone et al., Proc. Natl. Acad. Sci. USA 86:6077-6081, 1989), and purified transcription factors (Debs et al., J. Biol. Chem. 265:10189-10192, 1990), in functional form. Cationic liposomes are readily available. For example, N[1-2,3-dioleyloxy)propyl]-N,N,N-triethylammonium (DOTMA) liposomes are available under the trademark Lipofectin, from GIBCO BRL, Grand Island, N.Y. See also Felgner et al., Proc. Natl. Acad. Sci. USA 91: 5148-5152.87, 1994. Other commercially available liposomes include Transfectace (DDAB/DOPE) and DOTAP/DOPE (Boerhinger). Other cationic liposomes can be prepared from readily available materials using techniques well known in the art. See, e.g., Szoka et al., Proc. Natl. Acad. Sci. USA 75:4194-4198, 1978; and WO 90/11092 for descriptions of the synthesis of DOTAP (1,2-bis(oleoyloxy)-3-(trimethylammonio)propane)liposomes.
Similarly, anionic and neutral liposomes are readily available, such as from Avanti Polar Lipids (Birmingham, Ala.), or can be easily prepared using readily available materials. Such materials include phosphatidyl choline, cholesterol, phosphatidyl ethanolamine, dioleoylphosphatidyl choline (DOPC), dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl ethanolamine (DOPE), among others. These materials can also be mixed with the DOTMA and DOTAP starting materials in appropriate ratios. Methods for making liposomes using these materials are well known in the art.
One or more protein (e.g., a demethylaes) or nucleic acid (e.g., siRNA) of interest may be encoded by a single nucleic acid delivered. Alternatively, separate nucleic acids may encode different protein or nucleic acids of interest. Different species of nucleic acids may be in different forms; they may use different promoters or different vectors or different delivery vehicles. Similarly, the same protein or nucleic acid of interest may be used in a combination of different forms.
Antisense molecules, siRNA or shRNA molecules, ribozymes or triplex molecules may be contacted with a cell or administered to an organism. Alternatively, constructs encoding these may be contacted with or introduced into a cell or organism. Antisense constructs, antisense oligonucleotides, RNA interference constructs or siRNA duplex RNA molecules can be used to interfere with expression of a protein of interest, e.g., a histone demethylase. Typically at least 15, 17, 19, or 21 nucleotides of the complement of the mRNA sequence are sufficient for an antisense molecule. Typically at least 19, 21, 22, or 23 nucleotides of a target sequence are sufficient for an RNA interference molecule. Preferably an RNA interference molecule will have a 2 nucleotide 3′ overhang. If the RNA interference molecule is expressed in a cell from a construct, for example from a hairpin molecule or from an inverted repeat of the desired histone demethylase sequence, then the endogenous cellular machinery will create the overhangs. siRNA molecules can be prepared by chemical synthesis, in vitro transcription, or digestion of long dsRNA by Rnase III or Dicer. These can be introduced into cells by transfection, electroporation, or other methods known in the art. See Hannon, G J, 2002, RNA Interference, Nature 418: 244-251; Bernstein E et al., 2002, The rest is silence. RNA 7: 1509-1521; Hutvagner G et al., RNAi: Nature abhors a double-strand. Curr. Opin. Genetics & Development 12: 225-232; Brummelkamp, 2002, A system for stable expression of short interfering RNAs in mammalian cells. Science 296: 550-553; Lee N S, Dohjima T, Bauer G, Li H, Li M-J, Ehsani A, Salvaterra P, and Rossi J. (2002). Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature Biotechnol. 20:500-505; Miyagishi M, and Taira K. (2002). U6-promoter-driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells. Nature Biotechnol. 20:497-500; Paddison P J, Caudy A A, Bernstein E, Hannon G J, and Conklin D S. (2002). Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes & Dev. 16:948-958; Paul C P, Good P D, Winer I, and Engelke D R. (2002). Effective expression of small interfering RNA in human cells. Nature Biotechnol. 20:505-508; Sui G, Soohoo C, Affar E-B, Gay F, Shi Y, Forrester W C, and Shi Y. (2002). A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA 99(6):5515-5520; Yu J-Y, DeRuiter S L, and Turner D L. (2002). RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 99(9):6047-6052.
Antisense or RNA interference molecules can be delivered in vitro to cells or in vivo, e.g., to tumors of a mammal Typical delivery means known in the art can be used. For example, delivery to a tumor can be accomplished by intratumoral injections. Other modes of delivery can be used without limitation, including: intravenous, intramuscular, intraperitoneal, intraarterial, local delivery during surgery, endoscopic, subcutaneous, and per os. In a mouse model, the antisense or RNA interference can be adminstered to a tumor cell in vitro, and the tumor cell can be subsequently administered to a mouse. Vectors can be selected for desirable properties for any particular application. Vectors can be viral or plasmid. Adenoviral vectors are useful in this regard. Tissue-specific, cell-type specific, or otherwise regulatable promoters can be used to control the transcription of the inhibitory polynucleotide molecules. Non-viral carriers such as liposomes or nanospheres can also be used.
Exemplary siRNA or antisense molecules targeting LSD1 genes comprise the following nucleotide sequences or the complement thereof: 5′atgtcaaagatgagcagatt 3′ (SEQ ID NO: 38; which targest both mouse and human LSD1); 5′ggcgaaggtagagtacagaga 3′ (SEQ ID NO: 39; which targets human LSD1); and 5′ccatggttgtaacaggtctt 3′ (SEQ ID NO: 40; which targets mouse LSD1).
An exemplary siRNA or antisense molecule targeting human and mouse CoREST genes comprises the following nucleotide sequence or the complement thereof: 5′gacaatcttggcatgttggt 3′ (SEQ ID NO: 41).
An exemplary siRNA or antisense molecule targeting human BHC80 genes comprises the following nucleotide sequences or the complement thereof: 5′ ggacctcaaactgtacagctt 3′ (SEQ ID NO: 42).
Also provided herein are compositions, e.g., pharmaceutical compositions, and kits comprising one or more agent described herein. Kits may further comprise devices for administering the one or more agent to a subject. A device may be a syringe or a stent.
Exemplary Methods of Treatment and Diseases
Provided herein are methods of treatment or prevention of conditions and diseases that can be improved by modulating the methylation status of histones, and thereby, e.g., modulate the level of expression of methylation activated and methylation repressed target genes, such as an acetylcholine receptor, an SCN gene, p57 and genes regulated by the androgen receptor. A method may comprise administering to a subject, e.g., a subject in need thereof, a therapeutically effective amount of an agent described herein.
Diseases such as cancers and neurological disease can be treated by administration of modulators of histone methylation, e.g., modulators of histone demethylase enzyme activity. Histone methylation has been reported to be involved in overexpression of certain genes in cancers and of silencing of neuronal genes in non-neuronal cells. Modulators that are identified by the disclosed methods or modulators that are described herein can be used to treat these diseases, i.e., to restore normal methylation to affected cells.
Based at least on the fact that increased histone methylation has been found to be associated with certain cancers, a method for treating cancer in a subject may comprise administering to the subject a therapeutically effective amount of one or more agents that decrease methylation or restores methylation to its level in corresponding normal cells.
It is believed that modulators of methylation can be used for modulating cell proliferation generally. Excessive proliferation may be reduced with agents that decrease methylation, whereas insufficient proliferation may be stimulated with agents that increase methylation. Accordingly, diseases that may be treated include hyperproliferative diseases, such as bening cell growth and malignant cell growths.
Exemplary cancers that may be treated include leukemias, e.g., acute lymphoid leukemia and myeloid leukemia, and carcinomas, such as colorectal carcinoma and hepatocarcinoma. Other cancers include Acute Lymphoblastic Leukemia; Acute Lymphoblastic Leukemia; Acute Myeloid Leukemia; Acute Myeloid Leukemia; Adrenocortical Carcinoma Adrenocortical Carcinoma; AIDS-Related Cancers; AIDS-Related Lymphoma; Anal Cancer; Astrocytoma, Childhood Cerebellar; Astrocytoma, Childhood Cerebral; Basal Cell Carcinoma, see Skin Cancer (non-Melanoma); Bile Duct Cancer, Extrahepatic; Bladder Cancer; Bladder Cancer; Bone Cancer, osteosarcoma/Malignant Fibrous Histiocytoma; Brain Stem Glioma; Brain Tumor; Brain Tumor, Brain Stem Glioma; Brain Tumor, Cerebellar Astrocytoma; Brain Tumor, Cerebral Astrocytoma/Malignant Glioma; Brain Tumor, Ependymoma; Brain Tumor, Medulloblastoma; Brain Tumor, Supratentorial Primitive Neuroectodermal Tumors; Brain Tumor, Visual Pathway and Hypothalamic Glioma; Brain Tumor; Breast Cancer; Breast Cancer and Pregnancy; Breast Cancer; Breast Cancer, Male; Bronchial Adenomas/Carcinoids; Burkitt's Lymphoma; Carcinoid Tumor; Carcinoid Tumor, Gastrointestinal; Carcinoma of Unknown Primary; Central Nervous System Lymphoma, Primary; Cerebellar Astrocytoma; Cerebral Astrocytoma/Malignant Glioma; Cervical Cancer; Childhood Cancers; Chronic Lymphocytic Leukemia; Chronic Myelogenous Leukemia; Chronic Myeloproliferative Disorders; Colon Cancer; Colorectal Cancer; Cutaneous T-Cell Lymphoma, see Mycosis Fungoides and Sézary Syndrome; Endometrial Cancer; Ependymoma; Esophageal Cancer; Esophageal Cancer; Ewing's Family of Tumors; Extracranial Germ Cell Tumor; Extragonadal Germ Cell Tumor; Extrahepatic Bile Duct Cancer; Eye Cancer, Intraocular Melanoma; Eye Cancer, Retinoblastoma; Gallbladder Cancer; Gastric (Stomach) Cancer; Gastric (Stomach) Cancer; Gastrointestinal Carcinoid Tumor; Germ Cell Tumor, Extracranial; Germ Cell Tumor, Extragonadal; Germ Cell Tumor, Ovarian; Gestational Trophoblastic Tumor; Glioma; Glioma, Childhood Brain Stem; Glioma, Childhood Cerebral Astrocytoma; Glioma, Childhood Visual Pathway and Hypothalamic; Hairy Cell Leukemia; Head and Neck Cancer; Hepatocellular (Liver) Cancer, Adult (Primary); Hepatocellular (Liver) Cancer, Childhood (Primary); Hodgkin's Lymphoma; Hodgkin's Lymphoma; Hodgkin's Lymphoma During Pregnancy; Hypopharyngeal Cancer; Hypothalamic and Visual Pathway Glioma; Intraocular Melanoma; Islet Cell Carcinoma (Endocrine Pancreas); Kaposi's Sarcoma; Kidney (Renal Cell) Cancer; Kidney Cancer; Laryngeal Cancer; Laryngeal Cancer; Leukemia, Acute Lymphoblastic; Leukemia, Acute Lymphoblastic; Leukemia, Acute Myeloid; Leukemia, Acute Myeloid; Leukemia, Chronic Lymphocytic; Leukemia; Chronic Myelogenous; Leukemia, Hairy Cell; Lip and Oral Cavity Cancer; Liver Cancer, Adult (Primary); Liver Cancer, Childhood (Primary); Lung Cancer, Non-Small Cell; Lung Cancer, Small Cell; Lymphoma, AIDS-Related; Lymphoma, Burkitt's; Lymphoma, Cutaneous T-Cell, see Mycosis Fungoides and Sézary Syndrome; Lymphoma, Hodgkin's; Lymphoma, Hodgkin's; Lymphoma, Hodgkin's During Pregnancy; Lymphoma, Non-Hodgkin's; Lymphoma, Non-Hodgkin's; Lymphoma, Non-Hodgkin's During Pregnancy; Lymphoma, Primary Central Nervous System; Macroglobulinemia, Waldenström's; Malignant Fibrous Histiocytoma of Bone/Osteosarcoma; Medulloblastoma; Melanoma; Melanoma, Intraocular (Eye); Merkel Cell Carcinoma; Mesothelioma, Adult Malignant; Mesothelioma; Metastatic Squamous Neck Cancer with Occult Primary; Multiple Endocrine Neoplasia Syndrome; Multiple Myeloma/Plasma Cell Neoplasm' Mycosis Fungoides; Myelodysplastic Syndromes; Myelodysplastic/Myeloproliferative Diseases; Myelogenous Leukemia, Chronic; Myeloid Leukemia, Adult Acute; Myeloid Leukemia, Childhood Acute; Myeloma, Multiple; Myeloproliferative Disorders, Chronic; Nasal Cavity and Paranasal Sinus Cancer; Nasopharyngeal Cancer; Nasopharyngeal Cancer; Neuroblastoma; Non-Hodgkin's Lymphoma; Non-Hodgkin's Lymphoma; Non-Hodgkin's Lymphoma During Pregnancy; Non-Small Cell Lung Cancer; Oral Cancer; Oral Cavity Cancer, Lip and; Oropharyngeal Cancer; Osteosarcoma/Malignant Fibrous Histiocytoma of Bone; Ovarian Cancer; Ovarian Epithelial Cancer; Ovarian Germ Cell Tumor; Ovarian Low Malignant Potential Tumor; Pancreatic Cancer; Pancreatic Cancer; Pancreatic Cancer, Islet Cell; Paranasal Sinus and Nasal Cavity Cancer; Parathyroid Cancer; Penile Cancer; Pheochromocytoma; Pineoblastoma and Supratentorial Primitive Neuroectodermal Tumors; Pituitary Tumor; Plasma Cell Neoplasm/Multiple Myeloma; Pleuropulmonary Blastoma; Pregnancy and Breast Cancer; Pregnancy and Hodgkin's Lymphoma; Pregnancy and Non-Hodgkin's Lymphoma; Primary Central Nervous System Lymphoma; Prostate Cancer; Rectal Cancer; Renal Cell (Kidney) Cancer; Renal Cell (Kidney) Cancer; Renal Pelvis and Ureter, Transitional Cell Cancer; Retinoblastoma; Rhabdomyosarcoma; Salivary Gland Cancer; Salivary Gland Cancer; Sarcoma, Ewing's Family of Tumors; Sarcoma, Kaposi's; Sarcoma, Soft Tissue; Sarcoma, Soft Tissue; Sarcoma, Uterine; Sezary Syndrome; Skin Cancer (non-Melanoma); Skin Cancer; Skin Cancer (Melanoma); Skin Carcinoma, Merkel Cell; Small Cell Lung Cancer; Small Intestine Cancer; Soft Tissue Sarcoma; Soft Tissue Sarcoma; Squamous Cell Carcinoma, see Skin Cancer (non-Melanoma); Squamous Neck Cancer with Occult Primary, Metastatic; Stomach (Gastric) Cancer; Stomach (Gastric) Cancer; Supratentorial Primitive Neuroectodermal Tumors; T-Cell Lymphoma, Cutaneous, see Mycosis Fungoides and Sézary Syndrome; Testicular Cancer; Thymoma; Thymoma and Thymic Carcinoma; Thyroid Cancer; Thyroid Cancer; Transitional Cell Cancer of the Renal Pelvis and Ureter; Trophoblastic Tumor, Gestational; Unknown Primary Site, Carcinoma of Unknown Primary Site, Cancer of Unusual Cancers of Childhood; Ureter and Renal Pelvis, Transitional Cell Cancer; Urethral Cancer; Uterine Cancer, Endometrial; Uterine Sarcoma; Vaginal Cancer; Visual Pathway and Hypothalamic Glioma; Vulvar Cancer; Waldenström's Macroglobulinemia; Wilms' Tumor; and Women's Cancers.
Neurologic diseases that may be treated include epilepsy, schizophrenia, bipolar disorder or other psychological and/or psychiatric disorders, neuropathies, skeletal muscle atrophy, and neurodegenerative diseases, e.g., a neurodegenerative disease. Exemplary neurodegenerative diseases include: Alzheimer's, Amyotrophic Lateral Sclerosis (ALS), and Parkinson's disease. Another class of neurodegenerative diseases includes diseases caused at least in part by aggregation of poly-glutamine. Diseases of this class include: Huntington's Diseases, Spinalbulbar Muscular Atrophy (SBMA or Kennedy's Disease) Dentatorubropallidoluysian Atrophy (DRPLA), Spinocerebellar Ataxia 1 (SCA1), Spinocerebellar Ataxia 2 (SCA2), Machado-Joseph Disease (MJD; SCA3), Spinocerebellar Ataxia 6 (SCA6), Spinocerebellar Ataxia 7 (SCA7), and Spinocerebellar Ataxia 12 (SCA12).
Any other disease in which epigenetics, in particular methylation, plays a role is likely to be treatable or preventable by applying methods described herein.
Screening Methods
Also provided herein are screening methods for identifying agents that modulate methylation of a target protein, such as a histone, e.g., lysine 4 (K4) of histone 3.
One method comprises identifying an agent that modulates the interaction between a histone demethylase protein and a CoREST protein, comprising contacting a histone demethylase reagent and a CoREST reagent in the presence of a test agent; and (ii) determining the level of interaction between the histone demethylase reagent and the CoREST reagent, wherein a different level of interaction between the histone demethylase reagent and the CoREST reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the interaction between a histone demethylase protein and a CoREST protein. The method may further comprise at least one other component of a histone demethylase transcription complex. The method may also comprise determining the effect of the test agent on a biological activity of the histone demethylase. For example, a method may further comprise contacting a histone demethylase reagent and a CoREST reagent with the test agent and determining the biological activity of the histone demethylase reagent, wherein a different activity of the histone demethylase reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the biological activity of a histone demethylase.
A method for identifying an agent that modulates the biological activity of a histone demethylase may comprise: (i) contacting a histone demethylase reagent with a CoREST reagent in the presence of a test agent; and (ii) determining the biological activity of the histone demethylase reagent, wherein a different activity of the histone demethylase reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the biological activity of a histone demethylase. A higher activity indicates that the test agent is an agent that stimulates the biological activity of a histone demethylase. The biological activity of the histone demethylase reagent may be demethylase activity or amine oxidase activity. The CoREST reagent may comprise at least about amino acids 293 to 381 or 293 to 482 of human CoREST.
A method for identifying an agent that modulates the interaction between a histone demethylase protein and a BHC80 protein may comprise contacting a histone demethylase reagent and a BHC80 reagent in the presence of a test agent; and (ii) determining the level of interaction between the histone demethylase reagent and the BHC80 reagent, wherein a different level of interaction between the histone demethylase reagent and the BHC80 reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the interaction between a histone demethylase protein and a BHC80 protein. Step (i) may further comprise at least one other component of a histone demethylase transcription complex. The method may further comprise determining the effect of the test agent on a biological activity of the histone demethylase. The method may comprise contacting a histone demethylase reagent and a HDC80 reagent with the test agent and determining the biological activity of the histone demethylase reagent, wherein a different activity of the histone demethylase reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the biological activity of a histone demethylase.
A method for identifying an agent that modulates the biological activity of a histone demethylase may comprise: (i) contacting a histone demethylase reagent with a HDC80 reagent in the presence of a test agent; and (ii) determining the biological activity of the histone demethylase reagent, wherein a different activity of the histone demethylase reagent in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that modulates the biological activity of a histone demethylase. A higher activity indicates that the test agent is an agent that stimulates the biological activity of a histone demethylase. The biological activity of the histone demethylase reagent is demethylase activity or amine oxidase activity.
“LSD1 reagent”, “CoREST reagent” and “BHC80 reagent” refers to an LSD1, CoREST or BHC80 protein, homolog, or functional homolog thereof or portion thereof sufficient for use in the particular assay. For example, in an assay for determining whether two proteins interact, it is only necessary to include portions of those proteins that interact with each other.
Reagents may comprise at least a portion of a protein of interest, e.g., an LSD1, CoREST or BHC80 protein fused directly or indirectly to another moiety or label, e.g., a fluorophore or radioactive label or another peptide that may be useful in identifying, quantitating, isolating or purifying the reagent.
Other methods for identifying agents that modulate demethylase activity include methods using a reporter gene and a gene involved in methylation, e.g., LSD1, CoREST or BHC80. A method may comprise (i) providing a cell or cell lysate comprising an LSD1, CoREST or BHC80 gene or portion, e.g., promoter and/or enhancer, thereof, operably linked to a reporter gene and (ii) contacting the cell or cell lysate with a test agent and (iii) determining the level of expression of the reporter gene, wherein a higher level of expression of the reporter gene in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that increases the level of expression of the LSD1, CoREST or BHC80 gene, whereas a lower level of expression of the reporter gene in the presence of the test agent relative to the absence of the test agent indicates that the test agent is an agent that decreases the level of expression of the LSD1, CoREST or BHC80 gene. A reporter gene may encode firefly luciferase, chloramphenicol acetyltransferase, beta-galactosidase, green fluorescent protein, or alkaline phosphatase.
A screening assay described herein may further comprise testing the effect of the test agent on the demethylase activity in a cell. For example, a test reagent may be contacted with or administered into a cell and the level of expression of one or more genes whose expression is regulated by methylation may be measured. Alternatively, or in addition, the level of protein, e.g., LSD1, CoREST or BHC80 protein may be measured.
Test agents (or substances) for screening as inhibitors or enhancers of the demethylase enzymes can be from any source known in the art. They can be natural products, purified or mixtures, synthetic compounds, members of compound libraries, etc. The compounds to be tested may be chosen at random or may be chosen using a filter based on structure and/or mechanism of the enzymes. The test substances can be selected from those that have previously identified to have biological or drug activity or from those that have not. In some embodiments a natural substrate is the starting point for designing an inhibitor. Modifications to make the substrate non-modifiable by the enzyme can be used to make an inhibitor.
Also provided herein are compositions and molecular complexes comprising one or more proteins described herein. A composition may be a pharmaceutical composition.
All publications, including patents, applications, and GenBank Accession numbers mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.
The invention now being generally described, it will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present invention, and are not intended to limit the invention.
EXAMPLE 1
To understand the function and mechanism of action of KIAA0601, we undertook molecular, biochemical and enzymological analyses of the protein. Using multiple experimental approaches, we demonstrate that KIAA0601 is a lysine-specific demethylase with substrate specificity for K4 methylated histone H3. We now refer to protein as LSD1 (Lysine Specific Demethylase 1) to reflect this newly identified role. The text and figures corresponding to this example may be found in Shi et al. Cell (2004) 119:903, which is specifically incorporated by reference herein.
LSD1 is a Transcriptional Co-Repressor that is Evolutionarily Conserved
FIG. 1A shows a schematic diagram of the predicted domains of LSD1 and its related proteins. The C-terminal 2⁄3 of LSD1 display significant sequence homology with FAD-dependent amine oxidases. The N-terminus of LSD1 has a SWIRM domain, which is found in a number of proteins involved in chromatin regulation (Aravind and Iyer, 2002). Although the function of the SWIRM domain is currently unclear, the domain sets LSD1 and its family members apart from the conventional amine oxidases involved in metabolism. By searching for proteins that have both the amine oxidase and the SWIRM domains, we identified an LSD1-like protein AOF1 in human (FIG. 1A). In addition, we found three LSD-like proteins in C. elegans, one in Drosophila, five in Arabadoposis, and two in S. pombe (FIG. 1A). Some members such as SPAC23E2.02 of S. pombe contain an additional HMG box, suggesting possible DNA binding activity. The amino oxidase homology region was used for the construction of a phylogenetic tree shown in FIG. 1B. Interestingly, LSD1 homologs appear to be absent in S. cerevisiae. 
Since LSD1 has been found in a number of co-repressor complexes (Hakimi et al., 2002; Hakimi et al., 2003; Humphrey et al., 2001; Shi et al., 2003; Tong et al., 1998; You et al., 2001), we wished to determine whether it plays a direct role in transcriptional repression. We first asked whether LSD1 functions as a repressor when directed to a target promoter. When fused to the GAL4 DNA binding domain (G4LSD1), LSD1 repressed G4-TK-Luc reporter gene in a dose-dependent manner. As a control, G4 DNA binding domain alone (G4DBD) had no repressive effect on the same promoter and instead activated the promoter slightly. Furthermore, G4LSD1 had no effect on TK-Luc reporter lacking the G4 binding sites suggesting that repression was not due to squelching. Importantly, a C-terminal deletion mutant (G4LSD1ΔC) that lacks a large portion of the amine oxidase homologous region (diagrammed in FIG. 1C) and is therefore enzymatically inactive (see below) was significantly compromised in its ability to repress transcription, although some residual repression activity was observed for this mutant. Since repression mediated by LSD1 requires the C-terminal amine oxidase homology domain, the transcriptional function of LSD1 may therefore be linked to its enzymatic activity.
EXAMPLE 2
LSD1 is a Lysine-Specific Histone Demethylase
LSD1 is a flavin-containing protein based on its ability to bind FAD ((Humphrey et al., 2001), and data not shown). Its sequence homology with amine oxidases predicts that LSD1 may catalyze oxidation reactions of biogenic amines including monoamine, polyamines or N-methylated protein substrates (such as histones) (Bannister et al., 2002). Amine oxidation catalyzed by flavin-containing amine oxidase is characterized by oxidative cleavage of the a-carbon bond of the substrate to form an imine intermiediate, which, in turn, is hydrolyzed to form an aldehyde and amine via a non-enzymatic process. In a complete catalytic cycle, the cofactor FAD is reduced to FADH2 and then is likely to be re-oxidized by oxygen to produce hydrogen peroxide (Binda et al., 2002). We hypothesized that, as a flavin-containing amine oxidase homolog, LSD1 may catalyze the conversion of mono- or dimethylated K (or R) to non-methylated K (or R) and formaldehyde (FIG. 2). Since LSD1 is a transcriptional co-repressor, we further speculated that it might specifically remove methyl groups from lysine (or arginine) whose methylation is linked to active transcription. We chose to focus on H3-K4 methylation since this is one of the best-characterized sites where both di- and tri-methylation have been linked to active transcription (Liang et al., 2004; Litt et al., 2001; Noma et al., 2001; Santos-Rosa et al., 2002; Schneider et al., 2004). To investigate this possibility, a histidine epitope-tagged LSD1 (HIS-LSD1) was expressed in bacteria and purified to near homogeneity (FIG. 2). FAD was found to co-purify with LSD1 rendering the purified protein yellow, which is characteristic of FAD-bound proteins. The HIS-LSD1 proteins were incubated with histone H3 peptides carrying dimethylated K4 (diMeK4H3) or K9 (diMeK9H3) and the methylation status was determined using a diMeK4H3 or diMeK9H3 specific antibody, respectively. Even the lowest amount of LSD1 used (1 μg=10 pmole) effectively reduced dimethylation level at K4 (1 nmole of diMeK4H3) but had no effect on non-methylated H3. This represented approximately 1:100 molar ratio of LSD1 to diMeK4H3, consistent with this being an enzyme-driven reaction. In contrast, LSD1 failed to reduce the dimethylation level at K9, indicating substrate specificity of this enzyme. The significant reduction of the methylation signal on K4 in the presence of LSD1 was not due to degradation of the diMeK4H3 peptides since LSD1 had no affect on the stability of the H3 peptides. This putative enzymatic activity is abolished upon heat treatment, which caused protein denaturation, consistent with the possibility that LSD1 was the enzyme responsible for the observed demethylation. As a control, FMS1, which is an amine oxidase related to LSD1 in sequence, failed to catalyze the same enzymatic reaction. In contrast, FMS1 has previously been shown to catalyze oxidation of polyamine (Landry and Sternglanz, 2003). Importantly, HIS-LSD1 had barely detectable polyamine oxidation activity, yielding only a two-fold above background signal, which was about a thousand fold less active than FMS1. Therefore, LSD1 is likely a histone demethylase but not a polyamine oxidase. Significantly, the same C-terminal deletion mutant LSD1ΔC, which was compromised transcriptionally (FIG. 1E), also failed to demethylate diMeK4H3 peptides suggesting that LSD1-mediated transcriptional repression may be linked to this potential histone demethylase activity.
We next asked whether LSD1 can mediate demethylation reactions using native histones isolated from HeLa cells as substrates. Wild type LSD1, but, not LSD1ΔC, significantly reduced the signals detected by the diMeK4H3 antibody. The same blot was re-probed by a pan H3 acetylation antibody, which detected similar levels of acetylation with or without LSD1, suggesting that the loss of the methylation signal was not due to fortuitous degradation of histone H3. We next determined whether LSD1 could catalyze demethylation of histone H3 with either mono- or tri-methylated K4, the latter modification being also linked to active transcription. While LSD1 reduced the signal representing mono-methylated K4 of histone H3, it had no effect on trimethylated K4. The inability of LSD1 to convert tri-methylated K4 to an unmodified product is likely to be due to the inherent chemistry of the flavin-containing amine oxdases, which requires a protonated nitrogen in the substrates, thus restricting the substrates to mono- or dimethylated peptides (FIG. 2). The modification-specific antibodies used in the above assays were either commercial antibodies (see experimental procedures) or antibodies that have been reported in the literatures (e.g., anti-diMeK79H3 and anti-diMeK20H4 (Feng Q, 2002 and Fang J, 2002)).
To further determine the substrate specificity of LSD1, we examined a number of other amino acid residues on histones whose methylation is likely to be linked to active transcription, including K36 and K79 of histone H3 (Feng et al., 2002; Krogan et al., 2003; Ng et al., 2003a; Schaft et al., 2003), R2, R17 and R26 of histone H3 (Bauer et al., 2002; Chen et al., 1999; Schurter et al., 2001) and R3 of histone H4 (Strahl et al., 2001). We found no difference in the signal intensity detected by Western blotting, in the presence or absence of LSD1, using the modification-specific antibodies designed to visualize methylation at these sites, suggesting a high level of substrate specificity of this putative enzymatic activity. LSD1 also failed to remove the methyl groups from H3-K9, H3-K27 and H4-K20, modifications that are linked to transcriptional silencing (Cao et al., 2002, Czermin, 2002 #2921; Fang et al., 2002; Kuzmichev et al., 2002; Muller et al., 2002; Nishioka et al., 2002; Rea et al., 2000). Similar to the bacterially purified LSD1, endogenous LSD1 isolated from HeLa cells also displayed the same substrate specificity as the recombinant HIS-LSD1 protein. Taken together, these findings support our model that LSD1 functions as a transcriptional co-repressor by demethylating sites associated with active transcription but not repression.
To confirm the above results, we turned to mass spectrometry. As predicted by the chemical reaction outlined in FIG. 2, demethylation of a dimethyl-K4 histone H3 by LSD1 is expected to regenerate an unmodified histone H3 with the net loss of 28 Dalton equal to the molecular weight of 2 CH2. K4- and K9-dimethylated histone H3 peptides were incubated with purified HIS-LSD1, respectively, and the reaction mixtures were analyzed by mass spectrometry. The diMeK4H3 peptide peaked at molecular mass of 2863 Dalton as expected. Significantly, upon incubation with HIS-LSD1 but not HIS-LSD1ΔC, a new peak appeared at a molecular mass of 2835 Dalton that corresponded to the molecular weight of the unmodified histone H3 peptide. As a control, the K9-dimethylated H3 peptides were found to be unaffected by HIS-LSD1, consistent with the Western blotting results described earlier. Taken together these findings strongly suggest that LSD1 is a histone demethylase with a substrate preference for methylated K4 over K9 of histone H3.
EXAMPLE 3
LSD1-Mediated Histone Demethylation Generates Formaldehyde
We used a third independent method to investigate the possibility that LSD1 is a histone demethylase. As shown in FIG. 2, the demethylation reaction mediated by LSD1 is predicted to generate formaldehyde. To determine whether formaldehyde was produced in LSD1-mediated enzymatic reactions, we first used the formaldehyde dehydrogenase (FDH) assay to detect the presence of formaldehyde (Lizcano et al., 2000). This assay employs formaldehyde dehydrogenase to convert formaldehyde to formic acid using NAD+ as the electron acceptor, whose reduction to NADH can be spectrophotometrically measured at OD 340 nm. Thus, when the demethylation reaction is coupled with the FDH assay, the enzymatic activity of LSD1 and reaction kinetics can be determined by measuring the production of NADH. A standard curve was first generated using purified FDH (EC 1.2.1.46), NAD+ and different concentrations of formaldehyde ranging from 1 μM to 10 mM, within which a linear relationship was found between the production of NADH and the range of formaldehyde used in the assay. Subsequently, the coupled demethylation-FDH assays were carried out within this linear range and were initiated with the addition of the diMeK4H3 substrates. The continuous production of the formaldehyde as the demethylation proceeded was monitored by OD measurement at 340 nm at different time points. A robust increase of absorbance at 340 nm was observed within the first five minutes of the reaction, indicating that substantial amounts of formaldehyde were produced in the LSD1-catalyzed demethylation reaction. The fact that formaldehyde was generated in the demethylation reaction strongly suggests that the reaction had occurred as proposed in FIG. 2. Increasing the amount of either the enzyme (LSD1) or the substrates (diMeK4H3) in the demethylation reaction resulted in a dose-responsive increase in the conversion of NAD to NADH, respectively. We next used the demethylation-FDH coupled spectrophotometric assay as another independent means to investigate the substrate specificity of LSD1. Only when HIS-LSD1 was incubated with diMeK4H3, but not diMeR2H3 or diMeK9H3, did we detect a robust increase in the absorbance at OD 340 nm, indicating the production of formaldehyde and thus successful demethylation. Furthermore, we failed to detect formaldehyde when triMeK4H3 was used as substrate, suggesting that LSD1 is also unable to catalyze demethylation of the triMeK4H3 peptide. This result is consistent with the Western blotting assays using modification specific antibodies.
To further confirm the production of formaldehyde in the LSD1-mediated demethylation reaction, we next used Electrospray Ionization Liquid Chromatography-Mass Spectrometry (ESI-LC-MS) to detect formaldehyde. The formaldehyde produced in the demethylation reaction was captured by dimedone to irreversibly form the dimedone adduct, formaldemethone, which can be detected by the absorbance at OD 254 nm (Rozylo et al., 2000). The formaldemethone was eluted from an HPLC column and the mass of the formaldehyde derivative was analyzed by LC-MS. Using this assay, we identified formaldehyde in the LSD1-, but not LSD1ΔC-mediated demethylation reaction. Taken together, mass spectrometry and the FDH assay identified formaldehyde and unmodified histone H3 peptides as the products of the demethylation reaction catalyzed by LSD1.
EXAMPLE 4
LSD1 Regulation of Endogenous Target Gene Transcription and H3-K4 Methylation In Vivo
We next asked whether native LSD1 regulates endogenous target gene transcription and histone demethylation in vivo. Previous studies identified LSD1 in the Co-REST complex whose primary function is to silence neuronal specific genes in non-neuronal cells (Ballas et al., 2001). A number of Co-REST target genes have been reported including genes that encode the sodium channels (SCNs) and acetylcholine receptors (AchR) (Lunyak et al., 2002). We asked whether these promoters can be de-repressed when LSD1 was knocked down by DNA-vector based RNAi (Sui et al., 2002). The lsdl RNAi plasmid reduced LSD1 expression efficiently, as judged by immunostaining and Western blotting. Concomitant with the decrease in LSD1 expression, we observed an increase in M4 AchR, SCN1A, SCN2A and SCN3A expression as determined by RT-PCR. De-repression of these target genes in the LSD1 knockdown cells indicates that LSD1 is an essential component of the Co-REST complex and is likely to be required for silencing specific neuronal genes in non-neuronal cells. However, LSD1 targets are probably not limited to neuron-specific genes. We also identified p57KIP2, a cyclin-dependent kinase inhibitor (Lee et al., 1995), as a potential LSD1 target gene whose transcription also appeared to be negatively regulated by LSD1. Interestingly, p57KIP2 has recently been shown to play a role in developing dopamine cells (Joseph et al., 2003).
We next investigated whether LSD1 regulates histone demethylation in vivo. Using chromatin immunoprecipitation (ChIP), we found LSD1 located at the target gene promoters (within 2 kb of the transcription initiation site) in HeLa or control RNAi treated cells, but LSD1 promoter occupancy was significantly reduced in the lsdl RNAi cells.
Importantly, concomitant with the decrease of LSD1 occupancy at the target promoters, we observed an increase in H3-K4 dimethylation that coincided with the increase in the promoter activity. Thus, LSD1 promoter occupancy appears to be inversely correlated with promoter activity and H3-K4 dimethylation. Taken together, these findings support the hypothesis that LSD1 regulates histone K4 demethylation at specific loci in vivo, which is correlated with LSD1-mediated repression of target gene transcription.
EXAMPLE 5
We have provided multiple lines of evidence that support the conclusion that LSD1 is a histone lysine demethylase. These include the direct demethylation assays; mass spectrometry and the demethylation-FDH coupled spectrophotometric assays that revealed the demethylation products, i.e., demethylated histone peptides (mass spectrometry) and formaldehyde (FDH and mass spectrometry). We have also shown that LSD1 functions as a transcriptional co-repressor and plays an important role in restricting neuron-specific gene transcription in non-neuronal HeLa cells. Importantly, RNAi inhibition of LSD1 resulted in an increase in H3-K4 methylation, which is linked to active transcription, and a concomitant de-repression of the target genes, suggesting that LSD1 mediates transcriptional repression via histone demethylation in vivo.
Strikingly, as a histone demethylase, LSD1 displays stringent substrate specificity, which is manifested at two different levels. First, LSD1 is able to distinguish histone H3 peptides with the same type of methylation (dimethylation on lysine) that occurred on different lysine residues (K4 versus K9, K36 and K79). It is possible that the sequences surrounding these two lysine residues may contribute to this selectivity. Second, the substrate specificity of LSD1 is further highlighted by its ability to discriminate between di- and tri-methylation methylation on the same lysine H3-K4. The inability to demethylate triMeK4H3 is consistent with the chemical nature of the amine oxidation reaction catalyzed by flavin-containing amine oxidases, which requires a protonated nitrogen and thus precludes triMeK4H3 as a substrate (FIG. 2 and (Bannister et al., 2002)). This suggests that either triMeK4H3 turnover is accomplished by histone replacement or by an unidentified triMeK4H3-specific demethylase. Alternatively, additional mechanisms, such as direct hydroxylation of the methyl groups, may be involved in converting triMeK4H3 to an unmodified product. Our findings further suggest that additional histone demethylases are yet to be identified that would catalyze demethylation reactions at other lysine and/or arginine residues that are associated with either activation or repression of transcription.
Kinetic analysis of LSD1 provided further support that LSD1 is a histone demethylase. The apparent Km for the diMeK4H3 substrates is approximately 30 μM, which is comparable to other histone modifying enzymes such as the NAD-dependent histone deacetylase Sir2 (Boma et al., 2004). The actual Km for the demethylation reaction in mammalian cells is likely to be lower since not all purified HIS-LSD1 proteins are expected to be fully active. Possible posttranslational modifications of LSD1 as well as interacting proteins of LSD1 may further enhance its activity in mammalian cells. The fact that the physiological substrates of LSD1 in vivo are nucleosomes may also influence the activity of LSD1, as could other posttranslational modifications on histones. Regardless, these findings provide important kinetic information that substantiates the idea that LSD1 is a histone demethylase.
Another crucial piece of information that supports the conclusion that LSD1 is a histone demethylase is our ability to identify the demethylation reaction products, i.e. formaldehyde and the unmodified histone H3 peptides. Thus we have accounted for the major reaction products during an amine oxidase-mediated demethylation reaction. In this oxidation reaction, the cofactor FAD is likely to be reduced to FADH2 and then reoxidized to FAD by oxygen with the generation of H2O2. It will be important in the future to determine the fate of formaldehyde and H2O2, which could have potentially deleterious effects when present near promoters. Recently, a significant number of metabolic enzymes and coenzymes have been found to play central roles in regulating gene transcription (Shi, 2004). Further investigation of proteins such as LSD1 will provide insight into a possible direct link between metabolism and transcription.
Our finding that LSD1 regulates H3-K4 methylation at its target promoters but not global K4 demethylation (unpubl. result) suggests that LSD1 is a locus-specific histone demethylase. However, since LSD1 has been identified in numerous repressor complexes (Hakimi et al., 2002; Hakimi et al., 2003; Humphrey et al., 2001; Shi et al., 2003; Tong et al., 1998; You et al., 2001), we expect LSD1, much like the HDACs, to play a widespread and a central role in establishing repressive chromatin environment as a histone demethylase. We have previously shown that the CtBP repressor complex contains a number of potential enzymatic activities, including HDACs and HMTases that function coordinately to induce H3-K9 methylation, which is linked to transcriptional repression (Shi et al., 2003). We now show that another component of the CtBP complex, i.e., LSD1/nPAO, demethylates H3-K4 that is linked to active transcription. Taken together, these findings suggest that the establishment of a repressive environment mediated by the CtBP complex is likely to involve not only the process that confers the repressive modifications (HDACs and HMTases) but also events that erase histone modifications (LSD1) associated with active transcription. This level of complexity is consistent with the histone code hypothesis (Jenuwein and Allis, 2001) and is likely to represent a general principle underlying transcriptional regulation in eukaryotes. Lastly, in addition to H3-K9 methylation, H3-K4 hypomethylation has also been correlated with heterochromatin formation in S. pombe (Noma et al., 2001). It would be interesting to determine whether LSD1 homologs play a role in heterochromatin silencing as well as in euchromatic gene repression.
As with any fundamental biological processes, histone demethylation is expected to be conserved through evolution. In support of this hypothesis, we have identified LSD1 orthologs and homologs throughout the eukaryotic kingdom, ranging from S. pombe to human (FIG. 1). Curiously, LSD1-like proteins appear to be absent in S. cerevisiae where histone methylation also plays an important role in chromatin structure and transcriptional regulation. Thus, it is possible that S. cerevisiae may have evolved a different strategy to remove methyl groups from histones. Alternatively, different types of enzymes yet to be identified may be involved in demethylating histones in S. cerevisiae. In this regard, it is interesting to note that the S. cerevisiae genome, as do all the other eukaryotic genomes, has a large number of genes predicted to encode amine oxidases. It is possible that in addition to LSD1 family members, amine oxidases with a different architecture may also function as histone demethylases in S. cerevisiae and other organisms. Importantly, our findings documenting an amine oxidase functioning as a histone demethylase lays the foundation for investigation of other amine oxidases as candidates for histone demethylases. It will be exciting to determine if LSD1-related proteins and other types of oxidases function as histone demethylases with different substrate specificities to impact chromatin structure and gene transcription. Given our finding that histone demethylases exist, it will also be exciting to explore other types of enzymes that are also predicted to convert methylated peptides (such as histones) to unmethylated products (Chinenov, 2002).
Finally, recent studies provided a potential important connection between methylation at H3-K4 and cancer. The trithorax group protein MLL, which methylates H3-K4 is found to be frequently involved in chromosomal translocation in both acute lymphoid and myeloid leukemia (Ayton and Cleary, 2001). Another H3-K4 histone methylase, SMYD3, has been shown to be upregulated in colorectal and hepatocarcinoma cells (Hamamoto et al., 2004). Over-production of SMYD3 increases cell proliferation dependent on the histone methylase activity, consistent with the possibility that SMYD3 is a candidate oncogene (Hamamoto et al., 2004). These findings support the hypothesis that H3-K4 methylation regulation may play a crucial role in tumorigenesis. With the identification of LSD1 as a H3-K4 demethylase, we are now poised to investigate if LSD1 or related histone demethylases play a role in cancer, and if so, whether the demethylase activity is essential for this regulation.
EXAMPLE 6
Experimental Procedures
Peptides, histones, antibodies and chemical reagents. Synthetic histone peptides with specific modifications as well as antibodies (Ab) that recognize different histone modifications were purchased from either Upstate Group, INC (Lake Placid, N.Y.) (UP) or Abcam Ltd (Cambridge UK) (Ab). They are: diMeK4H3(1-21 aa) (UP12-460), diMeK9H3 (1-21aa) (UP12-430), H3 (1-21aa) (UP12-403), PanH3Ac (1-21aa) (UP12-402), anti-diMeK4H3 Ab (UP07-030), anti-diMeK9H3 Ab (UP05-768), anti-panH3Ac (UP06-599), anti-monoMeK4H3 Ab (UP07-436), anti-H3 Ab (UP06-755), anti-diMeR2H3 Ab (Ab8046), anti-diMeR3H4 (UP07-213), anti-diMeK79H3 Ab (UP07-366), anti-diMeR17H3 (UP07-214), anti-diMeR26H3 (UP07-215) and triMeK4H3 (Ab1342). Anti-diMeK36H3 and Anti-diMeK20H4 antibodies were gifts from Y. Zhang. Bulk histones were either purchased from Sigma (catalog # H9250) or isolated from HeLa cells according to the protocol provided by Upstate. Formaldehyde dehydrogenase (EC1.2.1.46) purified from Pseudomonas putida was purchased from Sigma (F1879). Purified recombinant yeast polyamine oxidase FMS1 was a kind gift from Dr. Rolf Sternglanz.
Protein expression and purification. Full length (1-851aa) and C-terminal deleted (1-427 aa) human LSD1 cDNAs were cloned into N-terminal 6× HIS-tag bacterial expression vector pET15b. The plasmids were transformed into bacteria and expression of the recombinant proteins was induced by 0.2 mM IPTG at 37° C. for 6 hours. The HIS-tagged proteins were purified by Ni-NTA affinity column (Qiagen, Valencia, Calif.). After washing the column, the bound proteins were eluted from the column by 200 mM imidazole. The eluate was then extensively dialyzed in PBS with 3 times change at 4° C. The homogeneity and concentration of the protein were estimated on SDS-PAGE by Commassie Blue staining using BSA as standard.
Demethylase assay. Bulk histones or histone peptides were incubated with purified HIS-LSD1 or HIS-LSD1ΔC in the histone demethylase activity (HDM) assay buffer 1 (50 mM Tris pH8.5, 50 mM KCl, 5 mM MgCl, 0.5% BSA and 5% glycerol) from 30 min up to 4 hours at 37° C. For a typical reaction, the volume of the reaction is 100 μl, in which either 20 μg of purified bulk histones or 3 μg of modified histone peptides were used as substrates. Different amounts of HIS-LSD1 ranging from 1-20 μg were used in the reaction. The reaction mixture was analyzed by SDS-PAGE/Western blotting using methyl-specific antibodies, or by formaldehyde formation assay to examine the removal and conversion of the methyl group to formaldehyde, or by mass spectrometry to identify the demethylated peptide.
MALDI Mass spectrometry (Matrix-assisted laser desorption/ionization mass spectroscopy). 2 μl of the 100 μl demethylation reaction mixture was desalted by passing through a C18 ZipTip (Millipore). Prior to desalting, the ZipTips were activated and equilibrated using 10 μl of 50% acetonitrile/0.1% TFA (2×), followed by 10 μl of 0.1% trifluoroacetic acid (TFA) (3×). The reaction mixture was then loaded onto the activated ZipTips. The ZipTips were washed with 10 μl of 0.1% TFA (5×), and the bound material was eluted from the ZipTip using 2 μl of 70% acetonitrile containing 1 mg/ml α-cyano-4-hydroxycinnamic acid MALDI matrix and 0.1% TFA. The eluates were spotted onto a circle of open MALDI target areas to allow solvent evaporation and peptide/matrix co-crystallization. The samples were analyzed by a MALDI-TOF/TOF mass spectrometer (Ultraflex, Bruker Daltonics, Billerica, Mass.) at the PFPC core facility of Department of Pathology, Harvard Medical School.
Formaldehyde Dehydrogenase (FDH) assay. Formaldehyde formation was continuously monitored by a coupled spectrophotometric assay (Lizcano et al., 2000) using formaldehyde dehydrogenase (FDH). HIS-LSD1 was first incubated in buffer containing 50 mM potassium phosphate, pH 7.2, 2 mM NAD+ and 0.1 U FDH (100 μl reaction volume) at 37° C. for 5 min without substrates. The demethylation-FDH coupled reaction was initiated by the addition of the substrates. The absorbance at 340 nm (ε340=6.22 mM−1 cm−1 for NADH) was measured at each time point in a 0.5 min interval using Beckman DU640 spectrophotometer. The OD 340 nm absorbance at the moment of the substrate addition was considered as 0 and this was used as the 0 min time point. Over a 10 min period, a kinetic software program automatically recorded the absorbance at each time point. The data were analyzed using the Excel program. Standard curves were obtained using various concentrations of formaldehyde diluted from 37% formaldehyde solution (Fisher). Km and Vmax values for the purified LSD1 catalyzing demethylation of the diMeK4H3 substrates were estimated using Lineweaver-Burk transformation of the Michaelis-Menten kinetic equation.
Electrospray Ionization-liquid chromatography-mass spectrometry (ESI-LC-MS). Standard formaldehyde or formaldehyde (FA) produced in the demethylation reaction was converted to formaldemethone (FDM) by the addition of dimedone, which has a strong absorbance at OD 254 nm and an increased mass suitable for MS detection. In a demethylation assay, 10 μg of enzyme and 15 μg of diMeK4H3 peptide were used in a 100 demethylation reaction. To convert FA to FDM, dimedone was added to the demethylation reaction (500 μl final volume with final concentration 0.0125%). For detection of FDM, samples were subjected to a reverse-phase high pressure liquid chromatography (HPLC) system (Agilent 1100) equipped with an analytical column (Waters Symmetry C18, 2.1×50 mm) at a flow rate of 0.4 ml/min. The HPLC system was directly coupled to a LCT mass spectrometer (MS) (Waters/Micromass). Analysis was performed in positive-ion electrospray (ESI) mode with acquisition across a mass range of 100 to 1000 daltons. The FDM were identified by the presence of a unique ion having a mass to charge ratio of 293.2, corresponding to the calculated molecular mass, with the addition of a single proton (M+H)+.
RT-PCR. Total RNA samples were isolated from 2×106 cells by Trizol reagent (Sigma). After DNase treatment, the RNA samples were purified by phenol-chloroform extraction and ethanol precipitation. 38 PCR cycles were used for SCN1A, SCN2A, SCN3A and M4 AchR and 28 PCR cycles for GAPDH. Primers used in RT-PCR were as follows: SCN1A up (5′-gcgaaatagcagaacaagcc-3′; SEQ ID NO: 1), down (5′-ctcattgctcgttgcctttg-3′; SEQ ID NO: 2); SCN2A up (5′-gatgaggatgatgaaaatggc-3′; SEQ ID NO: 3), down (5′-ctaattttctaatagggttgaaggg-3′; SEQ ID NO: 4) SCN3A up (5′-caccacttcctactttaatggca-3′; SEQ ID NO: 5), down (5′-aaatagagacaggaaagcccag-3′; SEQ ID NO: 6); p57KIP2 up (5′-ggcgatcaagaagctgtcc-3′; SEQ ID NO: 7), down (5′-caccttgggaccagtgtacc-3′; SEQ ID NO: 8); GAPDH up (5′-gaaggtgaaggtcggagtc-3′; SEQ ID NO: 9), down (5′-gaagatggtgatgggatttc-3′; SEQ ID NO: 10).
Chromatin Immunoprecipitation (ChIP) analysis. ChIP assays were carried out in IP buffer without SDS due to the sensitivity of the LSD1 antibody to SDS. Briefly, 3×107 cells were used per LSD1 ChIP and 3×106 cells per H3K4diMe ChIP. After 10 min 0.75% formaldehyde treatment, cells were harvested and sonicated in the ChIP lysis buffer (1% Triton X-100, 10 mM EDTA, 50 mM Tris-HCl and protease inhibitors) to produce soluble chromatin with average sizes between 300-1000 bp. The chromatin samples were then diluted 10 fold in the dilution buffer (5 mM EDTA, 25 mM Tris-HCl, 167 mM NaCl and cocktails of protease inhibitors) and pre-cleaned for 1 hour using salmon sperm DNA/protein-A agarose beads. 10 μg of rabbit anti-LSD1, 3 μl of anti-H3K4diMe or control antibodies were then added to each sample and incubated overnight at 4° C. To collect the immunocomplex, 40 μl of salmon sperm DNA/protein-A agarose beads were added to the samples for 1 hr at 4° C. The beads were washed 3× in the wash buffer 1(0.1% Triton X-100, 5 mM EDTA, 30 mM Tris-HCl, 150 mM NaCl) and 1× in wash buffer 2 (1% Triton X-100, 5 mM EDTA, 30 mM Tris-HCl, 300 mM NaCl). The bound protein-DNA immunocomplexes were eluted with 100 μl elution buffer (1% SDS, 0.1 M NaHCO3, 250 mM NaCl and 0.2 Protease K) and de-crosslinked at 65° C. for 4 hrs. The de-crosslinked chromatin DNA was further purified by QIAquick PCR Purification Kit (Qiagen) and eluted in 100 μl TE buffer. 4 μl of eluted DNA sample was used for each PCR reaction. 36 PCR cycles were used for LSD1 ChIP and 32 PCR cycles for H3K4diMe ChIP. Primers used for amplifications were as follows: M4 AchR forward (5′-gaacagaacacctccctcca-3′; SEQ ID NO: 11), reverse (5′-gagtcagaaggcaggacagg-3′; SEQ ID NO: 12); SCN1A forward (5′-taaagcccagtcaagacagc-3′; SEQ ID NO: 13), reverse (5′-gacacacccagaagatggag-3′; SEQ ID NO: 14); SCN2A forward (5′-cgtgtttcaaggctacagca-3′; SEQ ID NO: 15), reverse (5′-ctctagcctcccaaccttcc-3′; SEQ ID NO: 16); SCN3A forward (5′-ctctgtcacagggaggaaag-3′; SEQ ID NO: 17), reverse (5′-agactagagcaggccacaag-3; SEQ ID NO: 18); p57KIP2 forward (5′-ccgtggtgttgttgaaactg-3′; SEQ ID NO: 19), reverse (5′-tgtccggtggtggactatc-3′; SEQ ID NO: 20); GAPDH forward (5′-tcctcctgtttcatccaagc-3′; SEQ ID NO: 21), reverse (5′-tagtagccgggccctacttt-3′; SEQ ID NO: 22).
Sequence of KIAA0601 is SEQ ID NO: 23. The nucleotide sequence encoding KIAA0601 is SEQ ID NO: 24. The sequence of Histone H3 is SEQ ID NO: 25. The sequence of AOF1 protein is SEQ ID NO: 26 and the sequence of AOF1 coding sequence is SEQ ID NO: 27:
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The disclosure of each reference cited is expressly incorporated herein.
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EXAMPLE 7
Regulation of Lsd1 Histone Demethylase Activity by its Associated Factors
LSD1 is a recently identified human lysine (K)-specific histone demethylase. LSD1 is associated with HDAC1/2, CoREST, a SANT domain-containing co-repressor, and BHC80, a PHD domain-containing protein, among others. We show that CoREST endows LSD1 with the ability to demethylate nucleosomal substrates and protects LSD1 from proteasomal degradation in vivo. We find hyperacetylated nucleosomes less susceptible to CoREST/LSD1-mediated demethylation, suggesting that hypoacetylated nucleosomes may be the preferred physiological substrates. This raises the possibility that histone deacetylases and LSD1 may collaborate to generate a repressive chromatin environment. Consistent with this model, TSA treatment results in de-repression of LSD1 target genes. While HDAC1/2 and CoREST positively regulate LSD1 function, BHC80 inhibits CoREST/LSD1-mediated demethylation in vitro and may therefore confer negative regulation. Taken together, these findings suggest that LSD1-mediated histone demethylation is regulated dynamically in vivo, and this is expected to have profound effects on gene expression under both physiological and pathological conditions. The text and figures corresponding to this example may be found in Shi et al. Mol. Cell (2005) 19:1, which is specifically incorporated by reference herein.
The N-terminal tails of histones are subjected to multiple posttranslational modifications including methylation, which occurs on both lysine (K) and arginine (R) residues. Methylation on histone H3-K9 plays an important role in heterochromatin formation (Nakayama et al., 2001; Peters et al., 2002; Rea et al., 2000) as well as in euchromatin gene repression (Shi et al., 2003; Zhang and Reinberg, 2001). In contrast, methylation on the R and some K residues (such as H3-K4) is associated with active transcription (Kouzarides, 2002). Thus methylation represents a critical posttranslational modification of histones that impacts chromatin structure and gene transcription regulation (Bannister et al., 2002; Lachner and Jenuwein, 2002; Zhang and Reinberg, 2001).
Unlike other modifications that take place on histones such as acetylation and phosphorylation, methylation has long been thought to be a “permanent” modification. Challenging this current dogma, the recent discovery of the lysine specific histone demethylase LSD1 strongly suggests that histone methylation can be regulated dynamically via both histone methylases and demethylases (Shi et al., 2004). LSD1 (alias KIAA0601, p110b, npao and BHC110) is an amine oxidase, which mediates histone demethylation via an FAD-dependent oxidative reaction (Shi et al., 2004), and has been identified in a number of co-repressor complexes including CoREST, CtBP and a subset of HDAC complexes (Ballas et al., 2001; Hakimi et al., 2002; Hakimi et al., 2003; Humphrey et al., 2001; Shi et al., 2003; You et al., 2001). Consistent with these findings, LSD1 has been shown to function as a transcriptional co-repressor by demethylating K4 of histone H3 (Shi et al., 2004), where methylation is linked to active transcription (Liang et al., 2004; Litt et al., 2001; Noma et al., 2001; Santo-Rosa et al., 2002; Schneider et al., 2004). Interestingly, LSD1 has also been found in a histone H3-K4-specific methylase supercomplex (Nakamura et al., 2002), suggesting that LSD1 demethylation activity may be regulated in vivo. However, it has remained unclear if, when, and how LSD1 is regulated.
In this report, we address the issue of LSD1 regulation. We provide evidence that multiple factors associated with LSD1 regulate LSD1 histone demethylase function. Our findings suggest that LSD1-mediated histone demethylation is a step-wise, highly coordinated process that involves multiple LSD1-associated positive and negative regulatory factors including HDACs, CoREST and BHC80. These findings further suggest that LSD1-mediated histone demethylation is regulated dynamically in vivo, and this is expected to have profound effects on gene expression under both physiological and pathological conditions.
Results and Discussion
CoREST endows recombinant LSD1 with the ability to demethylate nucleosomal substrates. As described previously, bacterially purified LSD1 can demethylate mono- or dimethylated lysine 4 of histone H3 (H3-K4) when the substrate is either a histone peptide or free histone (Shi et al., 2004). In contrast, recombinant LSD1 was unable to demethylate nucleosomal substrates. Significantly, LSD1 purified from HeLa cells using the tandem affinity tag purification approach demethylated histones regardless of whether the substrates were bulk histones or histones assembled into the nucleosome. Mass spectrometry and Western blotting analysis identified a putative LSD1 complex (LSD1.com) containing HDAC1/2, CtBP1, CoREST, BHC80 and BRAF35, among others, and is essentially identical to the BHC110 complex reported previously (Hakimi et al., 2003). A difference is the presence of CtBP and absence of TFII-I in the LSD1 purification, compared with the previously reported BHC110 complex, but the reason for this discrepancy is currently unclear. The finding above suggested that either posttranslational modifications and/or factors present in the LSD1 complex contribute to the capability of LSD1 to modify a more complex substrate. To address this issue, we first asked whether factors in the LSD1 complex conferred upon LSD1 the ability to demethylate nucleosomal substrates. We investigated whether two LSD1 direct interacting proteins, CoREST and BHC80, played a role (Iwase et al., 2004; Jarriault and Greenwald, 2002) (Shi lab, unpubl. result). While the addition of bacterially purified HDAC1 and BHC80 had no effect, addition of CoREST to the demethylation reaction restored the ability of recombinant LSD1 to demethylate nucleosomal substrates. In contrast, CoREST has little stimulatory effect on the LSD1 demethylase activity when assayed on free histones using purified CoREST ranging from 0.3 to 5 μg.
CoREST contains two SANT domains (SANT1 and SANT2), which is a conserved protein motif found in a number of chromatin-associated proteins (Boyer et al., 2004; de la Cruz et al., 2005). The SANT domain in the co-repressor SMRT protein has been shown to preferentially interact with hypoacetylated histone tails (Yu et al., 2003). We speculated that the SANT domain(s) in CoREST might function similarly, thus making CoREST a candidate protein that may bridge the nucleosomal substrates and the demethylase LSD1. Consistent with this model, we found hyperacetylated nucleosomes isolated from HeLa cells treated with the HDAC inhibitor TSA less susceptible to CoREST/LSD1-mediated demethylation (approximately 4 fold difference in demethylation, comparing untreated with TSA-treated nucleosomes). This suggests that the HDACs in the LSD1 complex are likely to function upstream of CoREST/LSD1, generating a hypoacetylated histone substrate, which can then be better recognized by CoREST/LSD1. Further supporting this model, we found that inhibition of HDAC activity by TSA resulted in de-repression of two LSD1 target genes, the human neuronal-specific sodium channel (SCN) genes, SCNA2 and SCNA3. It should be noted that SCN2A expression was previously shown to be unaffected by TSA treatment in the Rat-1 fibroblast cells, suggesting possible species-specific regulation of LSD1 target genes (Lunyak et al., 2002). Regardless, our results suggest that HDACs play an important role in LSD1-mediated repression in vivo, and that HDACs may collaborate with LSD1/CoREST in HeLa cells to repress some of the REST target genes.
We next analyzed a series of N- and C-terminal CoREST deletion mutants (FIG. 3) in order to identify regions of CoREST that are important for stimulating the LSD1 demethylase activity. We found that deletion of the C-terminal region (aa 293 to 482) of CoREST had the most significant effect; i.e., it abrogated about 70% of the stimulatory function of CoREST. Importantly, the same C-terminal region is also sufficient to mediate stimulation of LSD1 demethylation activity to a level that is comparable to that of the wildtype CoREST, while the N-terminal CoREST (aa 1-293) had a weaker stimulatory activity ( ̃30% of the wildtype CoREST activity). Taken together, these findings show that majority of the stimulatory activity of CoREST can be attributed to the C-terminal region of CoREST.
To identify domains of CoREST that are involved in physical interactions with LSD1, GST-LSD1 or GST was incubated with bacterially purified, HIS-tagged CoREST and its mutant derivatives. After extensive washing, the bound and the follow-through fractions were analyzed by SDS PAGE and Coomassie Blue staining As predicted, the C-terminal domain of CoREST, del 2 (aa 293-482), which was sufficient to stimulate LSD1 activity, was also capable of binding LSD1. In addition to del2, del 3 (aa 105-381) and del 5 (aa 293-381) bound LSD1, but del 1 (aa 1-293) and del 4 (aa 105-293) did not, under the same assay conditions. This places the putative LSD1-binding domain within the C-terminal functional domain of CoREST, somewhere between aa 293-381 of CoREST. Interestingly, among the mutants that can bind LSD1 (del2, del3, del5), only del 2 stimulated LSD1 demethylation, indicating that physical interaction with LSD1 alone is not sufficient. A conspicuous difference between del2 and the mutants that bind LSD1 but fail to stimulate its activity is the SANT2 domain, which is present in del2 but not in del3 and del5 (FIG. 3). We therefore speculate that the SANT2 domain may be involved in mediate binding to the nucleosomal substrate. Taken together, these findings are consistent with the idea that CoREST functions as a bridging protein. The weak stimulatory activity of the N-terminal CoREST (del1, aa 1-293) remains unclear at the present time. Although we did not detect LSD1 binding to this region of CoREST, a low level of LSD1-binding activity can't be excluded. Interestingly, this region of CoREST also contains a SANT domain (SANT1), which, as discussed, has the potential to bind histone tails.
Previous studies identified spr-5 and spr-1 as C. elegans homologs of LSD1 and CoREST, respectively (Eimer et al., 2002; Jarriault and Greenwald, 2002). Mutations in either spr-5 or spr-1 suppress a presenilin mutation, suggesting that wildtype spr-5 and spr-1 normally function to repress Notch downstream target genes. The two mutations in spr-1 are nonsense mutations that are predicted to generate truncated spr-1 protein lacking the C-terminal region covering the area that corresponds to aa 340 to 482 of mammalian CoREST. Significantly, this is the same region we have shown to be important for stimulating LSD1 activity. Thus, both the genetic and biochemical data argued for a critical requirement of the C-terminal region of CoREST for stimulation of LSD1 activity.
CoREST regulates LSD1 stability in vivo. Having demonstrated that CoREST is crucial for LSD1 to mediate demethylation of nucleosomal substrates in vitro, we next wished to investigate the effect of loss of CoREST on LSD1-mediated transcription in vivo. We first inhibited CoREST expression by RNAi and unexpectedly found that a reduction of CoREST also led to a reduction of LSD1 expression Immunostaining of cells transfected with a CoREST shRNA plasmid showed that there was not only a significant reduction of CoREST but also LSD1 in  ̃80% of the CoREST shRNA-transfected cells as compared to control shRNA treated cells. This co-regulation was also observed when the transfected cells were analyzed by Western blotting. We found that the reduction of LSD1 protein expression was not at the RNA level since the LSD1 mRNA level remained the same in the presence or absence of the CoREST shRNA. Consistently, we found that the proteasome inhibitor ZL3VS (Kadlcikova et al., 2004) restored the LSD1 steady state level in CoREST shRNA treated cells close to that of the wildtype cells. Taken together, these findings show that when CoREST is absent or significantly reduced, LSD1 becomes prone to proteasomal degradation, suggesting that CoREST is required for LSD1 stability in vivo. These observations further suggest that there may be yet-to-be-identified mechanisms in place that regulate CoREST expression and/or CoREST/LSD1 interaction, which consequently impact LSD1-mediated H3-K4 demethylation and transcriptional repression. To begin to test this hypothesis, we determined H3-K4 methylation and LSD1 target gene transcription in cells where CoREST level was reduced by RNAi. CoREST shRNA resulted in de-repression of SCN2A and SCN3A, which have previously been shown to be LSD1 target genes (Shi et al., 2004). Importantly, we also observed a significant increase of H3-K4 dimethylation and a concomitant decrease of LSD1 at the target promoters by chromatin immunoprecipitation (ChIP). The reduced LSD1 promoter occupancy is likely to be due to a reduction of the LSD1 protein level in the CoREST shRNA cells.
BHC80 inhibits LSD1 demethylase activity in vitro. In addition to CoREST, the other protein in the LSD1 complex that can directly interact with LSD1, and therefore may influence LSD1 activity, is BHC80 (Hakimi et al., 2002; Iwase et al., 2004). As discussed earlier, BHC80 did not stimulate or inhibit LSD1 activity when it alone was assayed on nucleosomal substrates, under which condition LSD1 was largely inactive. We therefore asked whether BHC80 might exhibit any activity towards LSD1 when LSD1 is actively demethylating histones. While recombinant LSD1 efficiently demethylated H3-K4 on free histones, the addition of recombinant BHC80 significantly dampened this activity. BHC80 remained inhibitory regardless of whether CoREST was present or not in the free histone assays. We next asked whether BHC80 may display the same activity towards the active demethylase unit LSD1/CoREST on nucleosomal substrates. Similarly, while BHC80 had no effect on the inactive LSD1 (LSD1 alone assayed on nucleosomal substrate), increasing amounts of BHC80 caused a proportional decrease in the demethylase activity of LSD1/CoREST assayed on nucleosomal substrates. Thus, in contrast to HDAC1/2 and CoREST, which are positive regulators of LSD1 activity, the in vitro evidence presented above suggests that BHC80 may function to inhibit LSD1 activity.
In summary, we provided evidence in this study that LSD1-mediated histone demethylation is regulated by multiple factors associated with LSD1. CoREST protects LSD1 from proteasomal degradation and also plays an indispensable role for LSD1 to demethylate nucleosomal substrate in vitro. This predicts a critical role for CoREST in LSD1 function in vivo, which is supported by the ChIP data demonstrating that a reduction in the CoREST level significantly affects H3-K4 methylation at the LSD1 target promoters and their repression. HDACs, on the other hand, are implicated in the generation of hypoacetylated nucleosomes, which we show are more susceptible to CoREST/LSD1-mediated histone demethylation. Based on these findings, we speculate that HDACs and LSD1 functionally interact to generate a repressive chromatin environment. Specifically, we suggest that the process of LSD1-mediated H3-K4 demethylation is preceeded by HDACs, which cause histone hypoacetylation. The hypoacetylated histone H3 is preferentially recognized by CoREST, which bridges LSD1 to the nucleosomal substrates. Supporting this model, inhibition of HDAC activity by TSA caused de-repression of the LSD1 target genes SCNA2 and SCNA3. Lastly, although the in vivo function of the third component of the LSD1 complex, BHC80, is less clear, the fact that it inhibits LSD1-mediated histone demethylation in vitro suggests a possible negative regulatory mechanism that may provide negative feedback regulation and/or to limit LSD1 activity at the promoter.
The requirement for multiple factors in LSD1-mediated histone demethylation suggests possible dynamic regulation in vivo and predicts that signaling pathways or factors that can modulate LSD1 interactions with other proteins in the LSD1 complex such as CoREST and BHC80 may have profound effects on LSD1 activity in vivo. Importantly, this study has begun to shed light on the individual functions of the factors that are associated with LSD1, and lays the foundation for future exploration of signaling events that modulate these important interactions.
Experimental Procedures
Chemicals, antibodies and other reagents. Proteasome inhibitor ZL3VS was a kind gift from Dr. Hidde Ploegh's Lab (Harvard Medical School, Dept. of Pathology). Histone deacetylase inhibitor Trichostatin A (TSA) was purchased from Sigma. Antibodies (Ab) that recognize different histone modifications, namely anti-diMeK4H3 Ab (UP07-030), anti-diMeK9H3 Ab (UP05-768), anti-panH3Ac Ab (UP06-599), were purchased from Upstate Group, INC (Lake Placid, N.Y.) (UP). Anti-diMeK20H4 antibodies were gifts from Yi Zhang. Bulk histones were purchased from Sigma.
Preparation of mononucleosome. Mononucleosome was made according to a standard protocol (Tagami et al., 2004; Utley et al., 1996). Briefly, nuclear pellet from both TSA-treated or non-treated HeLa cells was homogenized for 60 times with type A pestle to obtain oligo-nucleosomes. The oligo-nucleosomes were then digested with micrococcal nuclease (40 units/mL) for 10 mins at 30° C. The nuclease is inactivated by 5 mM EDTA. Digested materials were spun at 14000 rpm for 3 mins. Resulting supernatant was spun again for additional 3 mins at the same speed. Supernatant from the second spin was subject to 10-25% glycerol gradient sedimentation. The monocleosome-containing fractions were identified by examining aliquots of fractions (treated with proteinase K) on DNA agarose gel. An aliquot of TSA-treated or non TSA-treated mononucleosome, a kind gift from Dr. Yoshihiro Nakatani's Lab in Dana Faber Cancer Institute, Harvard Medical School (Tagami et al., 2004), was used here as a control for the quality of mononucleosome made in our lab.
Recombinant protein expression, purification and GST pulldown assay. His-tagged full length (1-482aa) and deletion mutants of human CoREST were generated by PCR using pcDNA3.1-CoREST-myc plasmid as a template (A kind gift from Dr. Gail Mendal) and cloned into N-terminal 6× His-tag (SEQ ID NO: 50) bacterial expression vector and verified by DNA sequencing. The plasmid constructs were transformed into bacteria and the expression of the recombinant proteins was induced by 0.2 mM IPTG at 37° C. for 4 hours. His-tagged proteins were purified by Ni-NTA affinity column (Qiagen, Valencia, Calif.). After washing the column, the bound proteins were eluted from the column by 200 mM imidazole. The eluate was then extensively dialyzed in PBS for 3 times at 4° C. The homogeneity and concentration of the protein were estimated on SDS-PAGE gel followed by Coomassie Blue staining using BSA as standard. The primers used to generate CoREST wt and del mutants are as follows:








CoREST-WT:



P1



(cccgaattcatggtggagaagggccccgagt)
(SEQ ID NO: 44)


 


+P2



(cccctcgagtcaggaggcagatgcatatct);
(SEQ ID NO: 45)


 


CoREST-De11: P1 + P3



(cccctcgaggacctgaggaactgtctcagt);
(SEQ ID NO: 46)


 


CoREST-De12: P4



(cccgaattcactgagacagttcctcaggtc);
(SEQ ID NO: 47)


 


+P2



CoREST-De13 P5



(cccgaattcagggtcggaccccagtacca)
(SEQ ID NO: 48)


 


+P6



(cccctcgagccaacgtgcattacatttctga);
(SEQ ID NO: 49)


 


CoREST-De14: P5 + P3;



 


CoREST-De15: P4 + P6.







GST and GSTLSD1 plamsids were kind gifts from Dr. Tadashi Baba's Lab in Japan (Iwase et al., 2004). Expression and purification of GST and GSTLSD1 proteins were done using similar procedure as outlined for purification of his-tagged recombinant proteins. For GST-bead pulldown experiment, 2 μg of each purified his-tagged wt or del CoREST proteins were incubated with 5 μg of bound GST and GSTLSD1 proteins at 4° C. for 4 hrs in a binding buffer (50 mM Tris, pH 8.0, 300 mM NaCl, 1 mM DTT, 0.5 mM EDTA and 0.1% NP-40). The beads were washed 3 times in the binding buffer, resuspended in 2×SDS protein sample buffer, boiled for 5 mins and loaded onto 15% SDS PAGE gel. The gel was then stained with Coomassie Blue.
TAP protein complex isolation and identification. The detailed purification procedure has been described previously (Ogawa et al., 2002; Shi et al., 2003). In brief, Flag-HA-tagged human LSD1 was constructed in a retroviral expressing vector. Viruses containing the expressing cassette was made and transduced into HeLa cells. The Flag-HA-LSD1 stable cell line then was established and propagated as suspension cells. Nuclear extract was made from 30 L of cells, from which the LSD1 complex was purified by using anti-Flag M2 mAb-conjugated agarose beads (Sigma) followed by anti-HA 12CA5 mAb-conjugated agarose beads in buffer B (100 mM KCl, 20 mM Tris-HCl, pH 7.9, 5 mM MgCl2, 10% glycerol, 1 mM PMSF, 0.1% Nonidet P40, 10 mM 2-mercaptoethanol). The resulting LSD1 associated complex components were identified by MS/MS mass spectrometry as described previously (Shi et al., 2003).
Demethylation assay. LSD1 demethylation activity on free histone or nucleosomal histone was carried out as previously reported (Shi et al., 2004). Briefly, bulk histones or mononucleosomes were incubated with purified His-LSD1 with or without purified His-CoREST, His-CoREST mutants, His-BHC80 and/or GST-HDAC1 in the histone demethylase activity (HDM) assay buffer (50 mM Tris pH8.5, 50 mM KCl, 5 mM MgCl, 0.5% BSA and 5% glycerol) from 10 mins up to 1 hour at 37° C. The demethylase activity of LSD1 under various conditions was evaluated by Western blotting using K4-H3 methylation-specific antibodies.
Knockdown LSD, CoREST and Proteasome inhibitor (PI) treatment. Stable cell lines which express mutant GFP-shRNA, CtBP-shRNA, LSD1-shRNA or CoREST-shRNA were generated as previously described (Shi et al., 2003; Sui et al., 2002). To prevent proteasome-mediated protein degradation, the cells were treated with ZL3VS at final concentration 10 μM for 24 hours in culture then harvested. The protein and mRNA levels of the shRNA-knockdown cells with or without PI treatment were estimated by Western blotting and RT-PCR as previously described (Shi et al., 2004).
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Equivalents
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

## Claims

1. A method of increasing lysine methylation of a histone polypeptide in a cell, the method comprising contacting said cell with an agent that decreases the protein level or enzymatic activity of lysine specific demethylase 1(LSD1) or amine oxidase (flavin containing) domain 1(AOF1), wherein the agent decreases the protein level or enzymatic activity of LSD1 or AOF1 in the contacted cell compared to the protein level or enzymatic activity of LSD1 or AOF1 in the cell before the cell is contacted with the agent.

2. The method of claim 1, wherein the agent decreases the protein level of LSD 1 or AOF 1 in the cell.

3. The method of claim 1, wherein the agent decreases the enzymatic activity of LSD1 or AOF1 in the cell.

4. The method of claim 1, wherein said agent targets LSD1.

5. The method of claim 1, wherein said agent is a small molecule compound.

6. The method of claim 5, wherein said small molecule compound is a natural product compound or a synthetic compound.

7. The method of claim 1, wherein the increase in methylation comprises an increase in mono- or dimethylated lysine 4 of histone H3 (H3-K4).

8. The method of claim 1, wherein said agent is selected from a group consisting of: an siRNA molecule, a vector encoding a siRNA molecule, a shRNA molecule, a vector encoding a shRNA molecule, an antisense RNA molecule and a vector encoding an antisense RNA molecule.

9. The method of claim 8, wherein said molecule is a siRNA molecule.

10. The method of claim 8, wherein said siRNA molecule targets LSD1.

11. The method of claim 8, wherein said siRNA molecule comprises a sequence selected from the group consisting of SEQ ID NO: 38, SEQ ID NO: 39, and SEQ ID NO: 40.

12. The method of claim 1, wherein said cell is a mammalian cell.

13. The method of claim 1, wherein said cell is a human cell or a mouse cell.

14. The method of claim 1, wherein said cell is in an organism.

15. The method of claim 1, wherein said cell is selected from the group consisting of a cancer cell, a stem cell, and a neuronal cell.