METHODS OF TREATING NEURODEGENERATIVE DISORDERS COMPRISING DNA METHYLTRANSFERASE INHIBITORS
1. A method to reduce symptoms associated with neurodegenerative disorder in a subject, the method comprising administering to the subject a DNA methylation inhibitor.
The present disclosure provides a method of treating a neurodegenerative disorder, the method comprising administering a DNA methyltransferase inhibitor.
- 1. A method to reduce symptoms associated with neurodegenerative disorder in a subject, the method comprising administering to the subject a DNA methylation inhibitor.
- 7. A method to reduce mutant huntingtin protein (Htt)-induced neurotoxicity, the method comprising contacting a nucleoside analog DNA methyltransferase (DNMT) inhibitor to neurons.
- 11. A method of preventing the development of the symptoms associated with neurodegenerative disorder in a subject at risk of developing the neurodegenerative disorder, the method comprising administering to the subject a DNA methylation inhibitor.
- 14. The method of claim 14, wherein the DNMT inhibitor is decitabine or FdCyd.
This application claims the benefit of U.S. Provisional Application No. 62/349,484, filed Jun. 13, 2016 the disclosure of which is hereby incorporated by reference in its entirety.
This invention was made with government support under AG033724 awarded by the NIH. The government has certain rights in the invention.
The present invention encompasses compositions and methods of treatment for neurodegenerative disorders.
Neurodegenerative disorders are a collection of conditions which primarily affect the neurons in the human brain. These disorders are characterized by a progressive loss of structure or function of neurons, including death of neurons. Many neurodegenerative disorders, including amyotrophic lateral sclerosis, Parkinson'"'"'s, Alzheimer'"'"'s, and Huntington'"'"'s occur as a result of neurodegenerative processes.
Huntington'"'"'s disease (HD) in particular is a progressive and invariably fatal, autosomal-dominant neurodegenerative disorder characterized by progressive loss of selective neurons in the striatum and cortex, leading to movement, cognitive, and psychiatric disorders. HD is caused by an abnormal expansion of polyglutamine repeats in the huntingtin (Htt) protein. Formation of Htt aggregates is a hallmark of HD. How the toxic mutant protein drives neuronal dysfunction and death remains poorly understood, and no curative treatment exists for this disease. There is need in the art for better understanding and treatment of HD.
In one aspect the disclosure provides a method to reduce symptoms associated with neurodegenerative disorder in a subject, by administering a DNA methylation inhibitor to the subject. The neurodegenerative disorder treated may be HD. The DNA methylation inhibitor may be nucleoside analog DNA methyltransferase (DNMT) inhibitor. The DNA methylation inhibitor may be administered by the intracerebroventricular (icy) route.
In an aspect the disclosure provides a method to reduce mutant Htt-induced neurotoxicity, by contacting a nucleoside analog DNMT inhibitor to a neuronal cell. The DNMT inhibitor may be decitabine or FdCyd. The DNMT inhibitor may decrease the levels of mutant Htt aggregates.
In an aspect the disclosure provides a method of preventing the development of the symptoms associated with neurodegenerative disorder in a subject, the method comprising administering to the subject at risk of developing the neurodegenerative disorder with a DNA methylation inhibitor. The neurodegenerative disorder may be HD, and the subject may be at risk of developing HD. The DNMT inhibitor may be decitabine or FdCyd. The DNMT inhibitor may decrease the levels of mutant Htt aggregates.
The application file contains at least one drawing executed in color. Copies of this patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
The disclosure encompasses methods to treat neurodegenerative disorders in a subject by administering DNA methylation inhibitors. In particular, the disclosure provides methods of use for nucleoside analog DNA methyltransferase inhibitors to reduce the symptoms of and/or treat neurodegenerative disorder such as Huntington'"'"'s disease (HD).
Various aspects of the invention are described in further detail in the following subsections.
In one aspect the disclosure encompasses a composition comprising a DNA methyltransferase inhibitor. DNA methyltransferase inhibitors inhibit DNA methylation as catalyzed by a DNA methyltransferase. The term DNA methylation as used herein refers to the addition of a methyl group to the cytosine of a nucleotide. DNA methylation is catalyzed by members of the DNA methyltransferase (DNMT) family of enzymes, including DNMT1, DNMT3A, and DNMT3B.
Non-limiting examples of suitable DNA methyltransferase inhibitors may include decitabine, 5-fluoro-2′-deoxycytidine (FdCyd), azacitidine (also known as Vidaza™), zebularine, caffeic acid, chlorogenic acid, epigallocatechin gallate, hydralazine hydrochloride, procainamide hydrochloride, procaine hydrochloride, and N-phthalyl-L-tryptophan. In some embodiments, DNA methyltransferase inhibitors of the present disclosure may be nucleoside analog inhibitors. For instance, DNA methyltransferase inhibitors of the invention may be decitabine, FdCyd, azacitidine (also known as Vidaza™), or zebularine.
In an aspect, a DNA methylation inhibitor of a composition of the present disclosure is decitabine (
In another aspect, a DNA methylation inhibitor of a composition of the present disclosure is FdCyd (
In another aspect, a DNA methylation inhibitor of a composition of the present disclosure is azacitidine. A composition of the invention may comprise azacitidine at a concentration of about 0.02 uM to about 20 uM. In various aspects, a composition of the invention may comprise azacitidine a concentration from about 0.01 μM to about 0.05 μM, about 0.04 μM to about 1 μM, from about 0.8 μM to about 3 μM, from about 1 uM to about 10 μM, from about 5 μM to about 15 μM, or from about 10 μM to about 25 μM. Preferably the composition of the invention may comprise azacitidine at a concentration of 0.2 μM to 2 μM.
In another aspect, a DNA methylation inhibitor of a composition of the present disclosure is zebularine. A composition of the invention may comprise zebularine at a concentration of about 0.02 uM to about 20 uM. In various aspects, a composition of the invention may comprise zebularine a concentration from about 0.01 μM to about 0.05 μM, about 0.04 μM to about 1 μM, from about 0.8 μM to about 3 μM, from about 1 uM to about 10 μM, from about 5 μM to about 15 μM, or from about 10 μM to about 25 μM. Preferably the composition of the invention may comprise zebularine at a concentration of 0.2 μM to 2 uM.
In yet another aspect, a composition may include a combination of two or more DNA methyltransferase inhibitors. For instance, a composition may include two or more DNA methyltransferase inhibitors selected from the group consisting of decitabine, 5-fluoro-2′-deoxycytidine (FdCyd), azacitidine (also known as Vidaza™), and zebularine. In some embodiments, a composition may include three or more DNA methyltransferase inhibitors.
In yet another aspect a composition may include a DNA methyltransferase and a compound that increases the bioavailability or decreases the metabolism of the DNA methyltransferase. For instance, a composition may include a nucleoside analog DNA methyltransferase and a cytidine deaminase inhibitor that slows the metabolism of the nucleoside analog DNA methyltransferase to inactive metabolites. For instance, the composition may include FdCyd and a cytidine deaminase inhibitor tetrahydrouridine (THU) that inhibits metabolism and increases the bioavailability of FdCyd.
A suitable composition of the present disclosure may be a pharmaceutically acceptable composition. For instance, a composition may include a DNA methyltransferase inhibitor, and one or more pharmaceutically acceptable carriers, solvent, or excipients. For instance, suitable aqueous solvents may include any pharmaceutically acceptable aqueous solvent. In some embodiments, an aqueous solvent is sterile water for injection. In other embodiments, an aqueous solvent is a saline solution. Suitable saline solutions may be about 0.1% (w/v) to about 1% (w/v) sodium chloride. For example, a saline solution may be about 0.1% (w/v), about 0.2% (w/v), about 0.3% (w/v), about 0.4% (w/v), about 0.5% (w/v), about 0.6% (w/v), about 0.7% (w/v), about 0.8% (w/v), about 0.9% (w/v), about 1% (w/v) sodium chloride. These values can also be used to define a range, such as from about 0.1% (w/v) to about 0.5% (w/v) sodium chloride, about 0.25% (w/v) to about 0.75% (w/v) sodium chloride, or about 0.5% (w/v) to about 1% (w/v) sodium chloride. In yet other embodiments, an aqueous solvent is a dextrose solution. Suitable dextrose solutions may be about 2.5% (w/v) to about 5% (w/v) dextrose. For example, a saline solution may be about 2.5% (w/v), about 3% (w/v), about 3.5% (w/v), about 4% (w/v), about 4.5% (w/v), or about 5% (w/v). These values can also be used to define a range. In yet other embodiments, an aqueous solvent is Ringer'"'"'s Injection or Lactated Ringer'"'"'s Injection. In some embodiments, compositions of the invention may further comprise one or more pharmaceutically acceptable excipients suitable for parenteral administration and/or one or more additional active ingredients. Non-limiting examples of excipients may include preservatives, antioxidants, pH modifiers and buffers, chelating agents, antimicrobial agents, tonicity-adjusting agents, and combinations of any of these agents. The choice of suitable excipients will be influenced, in part, by the intended route of administration. Compositions formulated to be administered as a bolus in the intrathecal space typically will contain fewer, if any, preservatives, antioxidants, pH modifiers and buffers, chelating agents, antimicrobial agents, and tonicity-adjusting agents.
Non-limiting examples of preservatives or antioxidants may include, but are not limited to, ascorbic acid and its salts, ascorbyl palmitate, ascorbyl stearate, anoxomer, N-acetylcysteine, benzyl isothiocyanate, m-aminobenzoic acid, o-aminobenzoic acid, p-aminobenzoic acid (PABA), butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), caffeic acid, canthaxantin, alpha-carotene, beta-carotene, beta-caraotene, beta-apo-carotenoic acid, carnosol, carvacrol, catechins, cetyl gallate, chlorogenic acid, citric acid and its salts, clove extract, coffee bean extract, p-coumaric acid, 3,4-dihydroxybenzoic acid, N,N′-diphenyl-p-phenylenediamine (DPPD), dilauryl thiodipropionate, distearyl thiodipropionate, 2,6-di-tert-butylphenol, dodecyl gallate, edetic acid, ellagic acid, erythorbic acid, sodium erythorbate, esculetin, esculin, 6-ethoxy-1,2-dihydro-2,2,4-trimethylquinoline, ethyl gallate, ethyl maltol, ethylenediaminetetraacetic acid (EDTA), eucalyptus extract, eugenol, ferulic acid, flavonoids (e.g., catechin, epicatechin, epicatechin gallate, epigallocatechin (EGC), epigallocatechin gallate (EGCG), polyphenol epigallocatechin-3-gallate), flavones (e.g., apigenin, chrysin, luteolin), flavonols (e.g., datiscetin, myricetin, daemfero), flavanones, fraxetin, fumaric acid, gallic acid, gentian extract, gluconic acid, glycine, gum guaiacum, hesperetin, alpha-hydroxybenzyl phosphinic acid, hydroxycinammic acid, hydroxyglutaric acid, hydroquinone, N-hydroxysuccinic acid, hydroxytryrosol, hydroxyurea, rice bran extract, lactic acid and its salts, lecithin, lecithin citrate; R-alpha-lipoic acid, lutein, lycopene, malic acid, maltol, 5-methoxy tryptamine, methyl gallate, monoglyceride citrate; monoisopropyl citrate; morin, beta-naphthoflavone, nordihydroguaiaretic acid (NDGA), octyl gallate, oxalic acid, palmityl citrate, phenothiazine, phosphatidylcholine, phosphoric acid, phosphates, phytic acid, phytylubichromel, pimento extract, propyl gallate, polyphosphates, quercetin, trans-resveratrol, rosemary extract, rosmarinic acid, sage extract, sesamol, silymarin, sinapic acid, succinic acid, stearyl citrate, syringic acid, tartaric acid, thymol, tocopherols (i.e., alpha-, beta-, gamma- and delta-tocopherol), tocotrienols (i.e., alpha-, beta-, gamma- and delta-tocotrienols), tyrosol, vanilic acid, 2,6-di-tert-butyl-4-hydroxymethylphenol (i.e., lonox 100), 2,4-(tris-3′,5′-bi-tert-butyl-4′-hydroxybenzyl)-mesitylene (i.e., lonox 330), 2,4,5-trihydroxybutyrophenone, ubiquinone, tertiary butyl hydroquinone (TBHQ), thiodipropionic acid, trihydroxy butyrophenone, tryptamine, tyramine, uric acid, vitamin K and derivates, vitamin Q10, wheat germ oil, zeaxanthin, or combinations thereof. In an exemplary embodiment, the preservatives are an antioxidant, such as a-tocopherol or ascorbate, and antimicrobials, such as parabens, chlorobutanol or phenol.
Non-limiting examples of pH modifiers and buffers may include citric acid, acetic acid, tartaric acid, malic acid, fumaric acid, hydrochloric acid, lactic acid, phosphoric acid, sorbic acid, benzoic acid, sodium acetate, sodium borate, sodium carbonate, sodium bicarbonate, sodium phosphate, and potassium phosphate.
In some embodiments, a chelating agent may be included as an excipient to immobilize oxidative groups.
An antimicrobial agent may also be included as an excipient to minimize the degradation of the compound according to this disclosure by microbial agents, including but not limited to bacteria and fungi. Non-limiting examples of antimicrobials may include parabens, chlorobutanol, phenol, calcium propionate, sodium nitrate, sodium nitrite, Na2EDTA, and sulfites including but not limited to sulfur dioxide, sodium bisulfite, and potassium hydrogen sulfite.
Non-limiting examples of tonicity agents may include, but are not limited to, mannitol, dextrose, sodium chloride, sorbitol and boric acid. NaCl, glucose, and sucrose.
The pH of a pharmaceutically acceptable composition of the present disclosure will be influenced, in part, by the intended route of administration. In some embodiments, the pH is about 3, about 3.5, about 4, about 4.5, about 5, about 5.5, about 6, about 6.5, about 7, about 7.5 about 8, about 8.5, of about 9. In other embodiments, the pH is between about 4 and about 8, or between about 5 and about 8, or between about 6 and about 8. In still other embodiments, the pH is between about 4.5 and about 8, or between about 4.5 and about 7.5. In yet other embodiments, the pH is between about 5 and about 7.5, or between about 5.5 and about 8. In alternative embodiments, the pH is between about 5.5 and about 7.5. The pH of a pharmaceutical composition may be adjusted with acids or bases such as hydrochloric acid or sodium hydroxide, or by the addition of a pH modifier, as described above.
In an aspect, a composition of the present disclosure may include carriers, excipients, or solvents that are suitable for parenteral routes of administration including intravenous, intramuscular, intraperitoneal, subcutaneous, intradermal, intracerebralventricular, or other suitable routes of administrations known in the art. For instance, a composition may be administered in carriers, excipients, or solvents that are suitable for intracerebralventricular (icy) administration. Pharmaceutical compositions for effective administration are deliberately designed to be appropriate for the selected mode of administration, and pharmaceutically acceptable excipients such as compatible dispersing agents, buffers, surfactants, preservatives, solubilizing agents, isotonicity agents, stabilizing agents and the like are used as appropriate. Remington'"'"'s Pharmaceutical Sciences, Mack Publishing Co., Easton Pa., 16Ed ISBN: 0-912734-04-3, latest edition, incorporated herein by reference in its entirety, provides a compendium of formulation techniques as are generally known to practitioners. It may be particularly useful to alter the solubility characteristics of the compounds useful in this discovery, making them more lipophilic, for example, by encapsulating them in liposomes or by blocking polar groups.
In particular aspects of the present disclosure, a composition may include delivery vehicles designed to aid in crossing the blood-brain barrier of the subject, thereby increasing the availability of a composition to the neurons of a subject. Such delivery vehicles may include, for example, liposomes, lipophilic bubbles, and nanoparticles of different compositions known in the art. In further aspects, a composition may include components that increase the stability of the DNA methyltransferase inhibitors or minimize potential toxicity of an inhibitor. As will be appreciated by a skilled artisan, a variety of vehicles are suitable for delivering a composition of the present invention. Non-limiting examples of suitable delivery systems may include nanoparticles, liposomes, microemulsions, micelles, dendrimers and other phospholipid-containing systems. Methods of incorporating compositions into delivery vehicles are known in the art.
Generally speaking, a method of the present application may be used to treat neurodegenerative disorders. Suitable neurodegenerative disorders are those characterized, in part, by DNA methylation differences when compared to individuals who do not suffer from such disorders. Examples of neurodegenerative disorders that may be treated by a method of the present disclosure include Huntington'"'"'s disease (HD), Alzheimer'"'"'s disease (AD), Parkinson'"'"'s disease (PD), and amyotrophic lateral sclerosis (ALS). In an exemplary embodiment, the present application discloses a method to treat HD.
As used herein “treat” refers to reducing one or more symptoms of a neurodegenerative disorder. Non-limiting examples of specific neurodegenerative symptoms that may be reduced by a treatment of the present disclosure include motor, cognitive, and psychiatric symptoms. The motor symptoms of a neurodegenerative disorder may include involuntary muscle movement, impaired balance, impaired speech, and impaired eye movements. Cognitive symptoms may include impaired learning and thought processing. The psychiatric symptoms may include depression, insomnia, and fatigue.
The diagnosis of neurodegenerative disorders may be based, in part, on a physical and psychological examination by a physician, for the motor, cognitive, and psychiatric symptoms indicative of a neurodegenerative disorder. The diagnosis of a neurodegenerative disorder may also be aided by imaging techniques such as computerized tomography (CT) and magnetic resonance imaging (MRI) to detect cerebral abnormalities. Specific examples of such abnormalities may include neuronal atrophy or, for HD, Htt protein aggregates. The diagnosis of a neurodegenerative disorder may also be through functional neuroimaging with techniques such as fMRI and PET (Positron emission tomography) that reveals changes in brain activity due to neurodegeneration.
HD is also characterized by aggregation of the Huntingtin (Htt) protein. Aggregates of Htt may accumulate around the neurons of a subject with HD, and may lead to neurotoxicity. The neurotoxicity caused by the Htt aggregates, may lead to decreased function of the nervous system and may be responsible for the motor, cognitive, as well as psychiatric symptoms of HD.
The risk of developing neurodegenerative disorders may be evaluated by genetic testing, using a biological sample of a patient, such as blood. For HD, the HTT gene may be analyzed for an expansion mutation of the cytosine-adenine-guanine (CAG) triplet. The risk of developing HD may be evaluated especially in subjects whose parents have the disorder by genetic testing. The genetic testing for HD may also be performed prenatally using fetal amniotic fluid, in fetuses whose one or both parents have HD.
In an aspect, treatment may relieve the neurological symptoms associated with the neurodegenerative disorder. Treatment may result in partial or complete relief of symptoms motor, cognitive, or psychiatric symptoms. The decrease or relief of symptoms may be determined by a physical and psychological examination by a physician. The decrease in symptoms may also be determined by CT and/or MRI imaging or functional neuroimaging to determine decrease in neuronal atrophy, or improvement of brain functional activity. For instance, for HD, a decrease in symptoms may be represented by a decrease in Htt protein aggregates or improvement of brain functional activity.
In an aspect a method of treatment that prevents the development of symptoms of HD might be used. A subject evaluated at risk of development of HD may be administered the treatment as a preventive measure, to stop the development of symptoms, or to stop the progression of development of symptoms of HD.
In an aspect, treatment with a composition of the present disclosure may restore the expression of several key genes, including Bdnf. The treatment may restore the expression of Bdnf exon IX, IV and VI transcripts in neurons of the subject. In an aspect the treatment may upregulate the mRNA levels of key striatal genes known to be downregulated in HD. The striatal genes that may be upregulated by treatment are for example but not limited to brain derived neurotrophic factor (Bdnf), dopamine receptor D2 (Drd2), Protein phosphatase 1 regulatory inhibitor subunit IB (Ppp1r1b), and Adenosine A2a receptor (Adora2a). In an aspect the treatment may decrease Htt protein aggregates in a subject, the decrease in Htt protein aggregates may be evaluated by imaging techniques known in the art. A physician may assess the effectiveness of the treatment by evaluating cerebral images before and after treatment to evaluate the decrease of Htt protein aggregates in a subject.
In an aspect, the subject to be treated is a human subject. In other aspects, the subject to be treated may be any mammalian species that can exhibit symptoms of neurodegenerative disorder. For instance, the subject may be a human that exhibits symptoms of HD or be at risk of developing HD. Methods of identifying subjects that are suffering from a neurodegenerative disorder, or that are at risk of suffering from a neurodegenerative disorder, are known in the art.
In various methods of the present disclosure, a composition of the disclosure may be administered by intravenous, intramuscular, subcutaneous, intradermal, intraperitonial, or intranasal route of administration. In various methods of the present disclosure, a composition may also be administered into the brain of a subject by intraventricular route, by intracavitary route, into the interstitial system of the brain, or by intracerebral implantation. A composition may also be administered by any other route of administration known in the art that may contact a composition to cells of the brain. In preferred embodiments, a composition of the invention may be administered by methods that contacts one or more neurons of a subject. For instance, a composition of the invention may be administered by intraventricular, intracavitary, or into the interstitial system of the brain.
In a method of the present disclosure, a composition may be administered as a single injection (e.g. bolus administration), as a continuous infusion, or by an intracerebral implantation. In an aspect the interval between doses may be from less than about 1 day to about 4 days, from about 3 days to about 7 days, from about 5 days to about 10 days, from about 7 days to about 15 days, from about 14 days from about 28 days, from about 25 days to about 45 days, from about 30 days to about 60 days, and from about 50 days to about 70 days.
Generally, a compound will be administered in a therapeutically effective amount which includes prophylactic amounts or lower dosages for example, when combined with another agent. As used herein, “an effective amount” refers to doses of compound sufficient to provide circulating concentrations high enough to impart a beneficial effect on the recipient thereof. The precise amount to be administered can be determined by the skilled practitioner in view of desired dosages, side effects, and medical history of the patient.
In another aspect a method of treatment may include a combination therapy of the DNA methyltransferase inhibitors and other medications that reduce the motor, cognitive, and psychiatric symptoms of a neurodegenerative disorder. The other drugs used in combination may include for example but not limited to tetrabenazine, antipsychotic drugs, neuroleptics, mood stabilizers, and antidepressants. The treatment with DNA methyltransferase inhibitors may also be used in combination with other lifestyle therapies including for example but not limited to physical therapy and psychotherapy.
The following examples are included to demonstrate various embodiments of the present disclosure. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
To identify the critical epigenetic pathways that contribute to the death of mutant Htt-expressing neurons, we performed an epigenetic drug screen using a library composed of 84 epigenetic compounds with known targets, including writers, erasers, and readers of the epigenetic code (
To verify the effect of DNMT inhibition against mutant Htt toxicity, we next performed similar experiments with three other well-characterized nucleoside-analog DNMT inhibitors, 5-fluoro-2′-deoxycytidine (FdCyd), 5-azacytidine (azacitidine, 5-AC, Vidaza™), and zebularine. The latter two drugs are ribonucleoside analogs, which target primarily RNA rather than DNA, and small fractions of these drugs can be converted to their deoxyribose form in cells, thereby leading to inhibition of DNA methylation46, 47. 5-azacytidine, like decitabine, is a FDA-approved, potent anti-cancer drug that has been used for the treatment of MDS and AML. FdCyd was developed by the National Cancer Institute and is currently being investigated in ongoing clinical trials in solid tumors. Interestingly, the deoxyribonucleoside analog FdCyd, but not the ribonucleoside analogs, zebularine and 5-azacytidine, demonstrated neuroprotective effects against mutant Htt-induced toxicity in primary cortical neurons in cell viability and neurite degeneration assays (
To test if DNMTs play a role in the HD striatal neurons, one of the most severely affected cell types in the disease, we established a cultured striatal neuron model, in which the N-terminal exon-1 fragment of mutant or WT Htt was expressed by lentiviral infection. Strikingly, treatment with decitabine or FdCyd also attenuated mutant Htt-induced striatal neurite degeneration (
Because inhibition of DNMTs by decitabine and FdCyd rescued neurons from mutant Htt-induced toxicity, we next determined if molecular inhibition of DNMTs by RNA interference (RNAi) attenuates neuronal death in the mutant Htt context. Among members of the DNMT family, postmitotic neurons in the brain are known to highly express DNMT3A and DNMT127, 35, 36, 48. Knockdown of either DNMT3A or DNMT1 protein by lentiviral delivery of two distinct short hairpin RNAs (shRNAs) for each DNMT significantly increased the viability of mutant Htt-expressing cortical neurons (
BDNF is a major neurotrophic factor involved in fundamental brain processes, including neuronal survival, synaptic plasticity, and learning and memory. Bdnf mRNA and protein levels were found to be decreased in the brains of human HD patients and mouse models, which is thought to contribute to HD pathology11, 12, 15. Consistent with these observations, Bdnf expression was reduced by mutant Htt expression in primary cortical neurons (
Next, to test the hypothesis that abnormal DNA methylation contributes to the downregulation of Bdnf mRNA, we examined if pharmacological inhibition of DNMTs could rescue the expression of Bdnf exon IV and VI-containing mRNAs in mutant Htt-expressing cortical neurons by qRT-PCR analysis (
To verify these findings using an alternative HD model system, we next determined if decitabine could upregulate Bdnf mRNA expression in primary cortical neurons derived from bacterial artificial chromosome (BAC)-mediated HD transgenic (BACHD) mice, which express full-length mutant Htt53. BACHD mice exhibit progressive motor deficits and late-onset selective neuropathology in the cortex and striatum53. Inhibition of DNMTs by decitabine in BACHD mouse cortical neurons increased Bdnf exon IV- and VI-containing as well as total Bdnf (exon IX) mRNAs by qRT-PCR (
Because Bdnf exon IV and VI transcripts in mutant Htt-expressing cortical neurons are increased by DNMT inhibition (
DNA methylation-mediated gene repression is generally associated with a closed chromatin structure, which is induced by cooperation with altered histone modifications57. By chromatin immunoprecipitation (ChIP) analysis we found that the mutant Htt-triggered increase in DNA methylation is associated with decreased trimethylation at lysine 4 of histone H3 (H3K4me3), a transcriptionally active histone mark, in the promoter region of Bdnf exon IV in mutant Htt-expressing primary cortical neurons compared to WT Htt-expressing neurons (
Next, to further support the hypothesis that decreased Bdnf exon IV transcription by mutant Htt is the consequence of changes in DNA methylation at this locus, we examined whether inhibition of DNMTs in mutant Htt-expressing primary cortical neurons decreases DNA methylation in the regulatory region of Bdnf exon IV by MeDIP-qPCR. We found that inhibition of DNMTs by decitabine or FdCyd reversed the increase in DNA methylation triggered by mutant Htt (
Given the neuroprotective effect of decitabine in mutant Htt-expressing striatal neurons (
We next determined if DNMT inhibition could restore the expression of genes downregulated in HD in vivo using R6/2 HD mouse, a well-characterized transgenic mouse model expressing an N-terminal mutant Htt fragment60. This mouse model exhibits robust phenotypes with early disease onset and short life span and recapitulates the altered expression of a number of genes observed in HD patients, including Drd2 and Ppp1r1b in the striatum early in the course of disease progression12, 60, 61. Although decitabine has been reported to cross the blood-brain barrier62, 63, the cytosine nucleoside analog DNMT inhibitors, including decitabine and FdCyd, are known to be degraded rapidly by cytidine deaminase in the liver (in vivo half-life of decitabine <20 min)62, 64 indicating that systemic administration may not be an effective strategy for drug delivery to the brain. We therefore chose intracerebroventricular (icy) administration using an Alzet osmotic pump, which provides continuous infusion of drug at a consistent rate from a subcutaneous pump (
In this study, we have demonstrated that pharmacological or genetic inhibition of DNMTs substantially attenuates mutant Htt-induced transcriptional dysregulation and neurotoxicity in primary cortical and striatal neurons. We have also provided evidence that aberrant promoter methylation contributes to a reduction in Bdnf expression in mutant Htt-expressing cortical neurons. Given the neuroprotective effects of exogenous BDNF in HD model cortical neurons, blockade of DNMTs may protect neurons from mutant Htt-induced death in part through upregulation of Bdnf gene expression. Remarkably, in vivo experiments demonstrated that treatment of HD mice with DNMT inhibitor FdCyd could reverse the transcriptional repression of key striatal genes in HD mouse brain. Together, we provide evidence that DNA methylation in HD is a critical epigenetic mechanism, which underlies mutant Htt-induced transcriptional alterations and neurodegeneration, raising the possibility that the DNA methylation pathway might represent a new therapeutic target for HD.
Although the causal role of these epigenetic modifications in vulnerable neurons in HD remains unknown, our unbiased drug library screen with 84 chemical compounds, which target known epigenetic pathways, suggests that DNA methylation-mediated gene silencing plays a dominant role in triggering neuronal death.
In primary cortical neuron models, we found that mutant Htt induces increased DNA methylation in the regulatory region of Bdnf exon IV, which is associated with transcriptional repression and a reduction in the transcriptionally active H3K4me3 mark. Additionally, inhibition of DNMTs by pharmacological inhibitors or RNAi could rescue the expression of Bdnf exon IV mRNA in mutant Htt-expressing primary cortical neurons (
How mutant Htt promotes DNA methylation at specific Bdnf gene loci at the molecular level remains a significant open question. Possible mechanisms include: 1) mutant Htt expression in neurons increases the levels of DNMT expression, 2) mutant Htt enhances the activity of DNMTs, 3) mutant Htt facilitates the recruitment of the DNA methylation machinery to specific genomic regions, and/or 4) mutant Htt increases 5-mC levels by decreasing DNA demethylation activity in neurons. The first mechanism, however, is unlikely since we have found that mutant Htt does not significantly increase the mRNA or protein levels of DNMT1 or DNMT3A in primary cortical neurons. The second and third mechanisms are reasonable possibilities and may be caused by aberrant protein-protein interactions and/or abnormal posttranslational modifications of DNMTs downstream of mutant Htt. Regarding the fourth possible mechanism, whether mutant Htt increases 5-mC levels on repressed genes by inhibiting the DNA demethylation pathway in HD is an interesting question.
We focused on Bdnf as a model gene to test the hypothesis that mutant Htt represses neuronal gene expression through promoter hypermethylation. Our results show that mutant Htt expression increases cytosine methylation in the regulatory region of Bdnf exon IV and that inhibition of DNMTs reactivate exon IV transcription, supporting the idea that increased DNA methylation plays a causal role in repression of Bdnf transcription in HD. In contrast, the regulatory region of Bdnf exon VI, appears not to be directly regulated by DNA methylation, suggesting instead that indirect mechanisms are initiated by aberrant DNA methylation in the control of the Bdnf exon VI repression. Our results suggest that manipulation of DNA methylation may offer a new therapeutic approach to increase neuronal BDNF expression in HD brain.
The reduction of either DNMT1 or DNMT3A by RNAi is sufficient to block transcriptional changes and neuronal death induced by mutant Htt (
Finally, the findings from the current study immediately suggest that inhibition of DNMTs might ameliorate HD phenotypes in vivo, which will be the subject of important future experiments. Improved understanding of the epigenetic gene regulation in HD neurons will provide important foundational knowledge for the development of therapeutic strategies targeting DNA methylation abnormalities in HD.
Mouse monoclonal anti-neurofilament (NF) (165 kDa) (clone 2H3, Developmental Studies Hybridoma Bank) was used for immunofluorescence. Mouse monoclonal anti-β-actin (sc-47778, Santa Cruz Biotechnology), rabbit monoclonal anti-DNMT1 (D63A6, Cell Signaling Technology, Inc.), and rabbit polyclonal anti-DNMT3A (sc-20703, Santa Cruz Biotechnology) antibodies were used for immunoblotting. Mouse monoclonal anti-Htt (EM48) antibody85 (MAB5374, Millipore) was used for immunofluorescence and immunoblotting. Decitabine was purchased from Cayman Chemical (11166) and LC laboratories (D-3899). 5′fluoro-2′deoxycytidine (FdCyd) was purchased from Sigma (F5307) and Santa Cruz Biotechnology (sc-252267). These drugs were confirmed to exhibit similar effects regardless of the source.
Lentiviral expression plasmids containing Htt exon1-25Q (Htt-25Q) and Htt exon1-72Q (Htt-72Q) constructs under the control of the mouse PGK (Pgk1) promoter (mPGK-Httex1-25Q and mPGK-Httex1-72Q) were kindly provided by D. Krainc (Harvard Medical School, Boston, Mass.) (Northwestern University, Chicago, Ill.). Lentivirus-based Dnmt3a RNAi and Dnmt1 RNAi constructs (pLKO.1-puro), developed at the Broad Institute of MIT and Harvard, were obtained (Sigma-Aldrich). The oligo sequences in the shRNA vectors targeted Dnmt3a and Dnmt1 are as follows:
Mouse primary cortical and striatal neurons from embryonic day (E) 15.5 Swiss Webster mouse fetuses (Taconic) were first plated in the minimal essential medium (MEM) containing 10% FBS, 0.45% glucose, 1 mM sodium pyruvate, 2 mM glutamine, 20 U/ml penicillin and 20 μg/ml streptomycin, for 3 h and then maintained in serum-free Neurobasal medium (Life Technologies) containing NeuroCult™ SM1 neuronal supplement (STEMCELL Technologies), 0.5 mM glutamine and 25 μM glutamate for the first 3 d in a humidified incubator (37° C. in 5% CO2). Half of the medium was replaced with Neurobasal medium with SM1 and 0.5 mM glutamine every 3 days. Primary cortical neurons plated on 96-well flat clear bottom black plates (Corning #3904) at 4×104 cells/well were infected with Htt exon1 expression lentivirus (Htt-25Q or Htt-72Q) or control empty vector lentivirus at 5 days in vitro (DIV 5). Primary striatal neurons plated on 96-well plates at 1×105 cells/well were infected with Htt exon1 expression lentivirus at DIV 4. Viral copy number was adjusted for transduction of neurons on the basis of titer measured using the Lenti-X qRT-PCR titration kit (Clontech), and equal numbers of viral particles of Htt-25Q and Htt-72Q expressing lentiviruses were used for transduction. For the experiments to test effects of DNMT inhibitors, neurons were treated with inhibitors six hours after Htt lentiviral infection. One half of the media was changed every 3 days with media containing new drug. In knockdown experiments in Htt-expressing neurons, primary cortical neurons were cotransduced with Htt-expressing lentivirus and Dnmt shRNA or control shRNA lentivirus at DIV 5. pLKO.1-TRC1-luciferase (Luci) and pLKO.1-TRC2-LacZ were used as control for RNAi with pLKO.1-TRC1-Dnmt3a and pLKO.1-TRC2-Dnmt1, respectively. Lentiviral particles were prepared by transfecting 293LE cells with the lentiviral plasmid of interest along with packaging plasmid psPAX2 and envelope plasmid pCMV-SVG as described previously86. Four days after transfection, viruses in the conditioned media were collected and purified using Lenti-X Concentrator (Clontech). Primary cortical neurons from BACHD mouse embryos (E15.5) were individually plated into separate wells and treated at DIV 4 with decitabine or vehicle for 3.5 days.
Primary cortical neurons grown in a 96-well plate were transduced with Htt-expressing lentiviruses at DIV 5 and assessed for mitochondrial metabolic activity at 9 days post-infection (DIV 14) using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) (Promega) per manufacturer'"'"'s instructions. MTS-reducing activity was normalized for each condition to Htt-25Q lentiviruses treated with vehicle or cotransduced with control RNAi lentivirus (=1). Experiments were performed in 3 or more wells per experiment in three to five independent experiments.
For the measurement of neurofilament (NF) immunofluorescence intensity, cortical and striatal neurons cultured in a 96-well plate were fixed in 4% paraformaldehyde (PFA) in PBS for 20 min nine and seven days after Htt lentiviral infection, respectively, permeabilized with 0.1% Triton X-100 in PBS for 15 min at room temperature, and subjected to indirect immunofluorescence with anti-NF (2H3) primary antibody and Alexa Fluor 568-conjugated goat anti-mouse IgG secondary antibody (Life Technologies). Images of Alexa Fluor 568 and bright field were captured (nine random fields per well) using an Operetta high-content imaging system (PerkinElmer) with a 20× objective lens. Following image background subtraction, the NF immunofluorescence intensity was quantified using an ImageJ-based macro. Image capture and quantification of Htt (EM48) immunofluorescence intensity were performed as described for those of NF. In this quantification analysis, we confirmed that the number of cells in a cultured well are similar among mutant Htt-expressing neurons with or without DNMT inhibitor treatment, by counting the number of nuclei in the images used for quantification: Htt-72Q neurons treated with vehicle (299±7.8 cells), decitabine (299±4.6 cells), n=18 wells from 6 independent experiments, and therefore the data reflect EM48 intensity per cell. For the quantification of cell death, primary cortical neurons grown in a 96-well plate were infected with Htt lentivirus at DIV 5 and fixed nine days after infection as described above. Cell nuclei were labeled with Hoechst 33342 (Life Technologies), and neurons were assessed in a blinded fashion for cell death by scoring condensed or fragmented nuclei. Experiments were performed in 4 to 6 wells per experiment in three independent experiments. About 300 nuclei from three random fields in a well were counted.
Epigenetic drug screen was performed using a primary cortical neuron model of HD with a drug library composed of 84 compounds (Table 1), among which 80 drugs are purchased from Cayman Chemical (Epigenetic Screening Library Item No 11076) and four drugs, SGC0946, EPZ5676, EPZ6438, and GSK126, were obtained from Xcessbio Biosciences Inc. Mouse primary cortical neurons were plated on 96-well flat clear bottom black plates (Corning #3904). WT or mutant Htt exon1 fragment (Htt-25Q or Htt-72Q)-expressing lentiviruses are infected at DIV 5 as described above. The 84 compounds were added to the media at DIV 6 one day after Htt lentiviral infection with three different doses (0.02, 0.2, 2 μM) for each compound at triplicates. DMSO was used as control. Media containing compounds or DMSO were changed every three days to maintain the compounds'"'"' activity. At DIV 14, the viability of neurons was determined by resazurin (Alamar blue) assay, a quantitative measurement of mitochondrial metabolic activity. The screen was fully automated and performed in the High-Throughput Screening Center in Washington University School of Medicine. Any possible plate effects were determined using control plates treated with DMSO and used for normalization. Screen hits were validated by MTS assay.
R6/2 mice, which carry the promoter sequence and exon 1 of a mutant human HTT gene, were obtained from JAX (Stock No: 002810) (Bar Harbor, Me.), and a colony was maintained by breeding R6/2 males with B6CBAF1 females (JAX). PCR genotyping was performed using a primer set (CGGCTGAGGCAGCAGCGGCTGT (SEQ. ID NO:5) and GCAGCAGCAGCAGCAACAGCCGCCACCGCC(SEQ ID NO:6)) as described [Mangiarini, L. et al. 1996 Cell]. To maintain mice carrying the same number of CAG repeats, a second PCR analysis was also conducted using a primer set amplifying across the CAG repeats (ATGAAGGCCTTCGAGTCCCTCAAGTCCTTC (SEQ ID NO: 7) and GGCGGCTGAGGAAGCTGAGGA (SEQ ID NO: 8)). BACHD mice on the C57BL6/J background, which were generated by the laboratory of X. William Yang (University of California, Los Angeles)53, 87, were obtained from the CHDI Foundation. All live vertebrate experiments were performed in compliance with the US National Institutes of Health Guide for the Care and Use of Laboratory Animals. Animal protocols were approved by the Institutional Animal Care and Use Committees of Washington University. To determine the effect of DNMT inhibitor on gene expression in HD mouse brain in vivo, FdCyd (0.1 mM in saline) was directly administered into 6 week-old R6/2 mice and control littermates by stereotactic intracerebroventricular (icy) infusion using Alzet mini-osmotic pump (DURET Corporation, MODEL 2001; 1.0 μl/h, 7 days) and the brain infusion kit 3 (DURET Corporation, #0008851). Saline was used as control. One week later, the striatum was dissected and processed for qRT-PCR analysis. The CAG repeat length of R6/2 mice used for the in vivo gene expression analysis was determined by Laragen Inc. (Culver City, Calif.) using tail DNA and was approximately 200.
Quantitative Reverse Transcription PCR (qRT-PCR)
RNAs were isolated from cultured neurons 5 days after infection of Htt lentiviruses and mouse brain using the RNeasy Plus Mini Kit (QIAGEN) and RNeasy Plus Universal Mini Kit (QIAGEN), respectively. Reverse transcription was performed with High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems). qPCR was performed using Power SYBR Green PCR Master Mix (Applied Biosystems) on CFX Connect Real-Time System (Bio-Rad). β-actin and hypoxanthine phosphoribosyltransferase I (Hprt), and/or 18S rRNA were used as reference genes for data normalization unless otherwise stated. Relative mRNA levels were calculated using the ΔΔCq method. Sequences of the primers used for qRT-PCR analysis are listed in Table 2 (SEQ ID NOs: 9-46).
Genomic DNA was extracted from cells using QIAamp DNA Mini Kit (QIAGEN) and subjected to bisulfite conversion using EZ DNA Methylation-Lightning™ Kit (Zymo Research) according to the manufacturer'"'"'s instructions. Gene regulatory regions for Bdnf exons IV and VI were PCR amplified using ZymoTaq™ DNA Polymerase (Zymo Research) from the bisulfite-converted DNA templates. The PCR fragments were subcloned into the pCR2.1-TOPO vector using TOPO TA cloning kit (Life Technologies) and sequenced with M13 primer (Genewiz). The primers used for PCR amplification of the bisulfite-converted genomic DNA are listed in Table 2 (SEQ ID NOs: 47-50).
Genomic DNA was isolated from primary cortical neurons using QIAamp DNA Mini Kit (QIAGEN) and fragmented by sonication using Bioruptor (Diagenode). 5-mC-containing DNA fragments were enriched from one μg of the sonicated genomic DNA by immunoprecipitation (IP) with mouse monoclonal anti-5mC antibody (Eurogentec, # BI-MECY-0100) as described previously88. IP and 10% input DNA samples were purified using MinElute PCR Purification Kit (QIAGEN) and subjected to qPCR with Bdnf promoter IV and Gapdh primers to measure the enrichment of the DNA fragment containing the Bdnf promoter IV region. Primer sequences are provided in Table 2 (SEQ ID NOs: 51-54). The percentage input was calculated by first normalizing IP to input DNA using the formula (2[(Ct(10% input)-3.32)-Ct(IP)]×100) as described previously89. Gapdh was used as an internal normalization control.
ChIP assays from mouse primary neurons were performed using Magna ChIP kit (Millipore) and anti-H3K4me3 antibody (Millipore, 17-614). The percentage input was calculated as 2[(Ct(10% input)-3.32)-Ct(IP)]×100 and compared between WT and mutant Htt-expressing neurons. Sequences of the primers used to amplify the BDNF promoter IV fragment are listed in Table 2 (SEQ ID NOs: 55-56).
Statistical differences were tested using XLSTAT and GraphPad Prism 6.0. Two-tailed unpaired Student t test for two group comparisons or one-way ANOVA with post-hoc tests, the Fisher'"'"'s least significant difference (LSD) for comparison among three groups or the Bonferroni analysis for comparison among three or more than three groups. The Mann-Whitney U test was used for nonparametric test for comparing two groups. The data presented are from at least three independent experiments.
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