US20170354666A1 - Compositions and methods for treating lysosomal disorders - Google Patents

Compositions and methods for treating lysosomal disorders Download PDF

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US20170354666A1
US20170354666A1 US15/527,506 US201515527506A US2017354666A1 US 20170354666 A1 US20170354666 A1 US 20170354666A1 US 201515527506 A US201515527506 A US 201515527506A US 2017354666 A1 US2017354666 A1 US 2017354666A1
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disease
tfeb
pparα
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fibrate
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Kalipada Pahan
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Rush University Medical Center
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Definitions

  • the present invention generally relates to compositions and methods for treating lysosomal storage disorders.
  • Lysosomes are membrane bound organelles containing a host of hydrolytic enzymes that are highly active in acidic milieu (1-3).
  • TFEB Transcription Factor EB
  • MiT/TFE microphthalmia-transcription factor E
  • Tfeb The regulation of Tfeb appears to be complex and dependent on cell type and stimuli.
  • a RANKL-dependent signaling pathway induces TFEB activation induced lysosomal biogenesis (13).
  • Starvation or stress conditions may also activate TFEB, which otherwise is maintained in an inactivated state by mTORC1 (14, 15).
  • mTORC1 14, 15
  • starvation induced TFEB activity can play a vital role in lipid metabolism and that activated TFEB can also autoregulate its own gene expression (16).
  • Lysosomal storage diseases are a group of approximately 50 rare inherited metabolic disorders that result from defects in lysosomal function.
  • the symptoms of LSD vary, depending on the particular disorder and other variables like the age of onset, and can be mild to severe. They can include developmental delay, movement disorders, seizures, dementia, deafness and/or blindness.
  • Some people with LSD have enlarged livers (hepatomegaly) and enlarged spleens (splenomegaly), pulmonary and cardiac problems, and bones that grow abnormally.
  • One aspect of the present invention provides a method for treatment of a LSD.
  • the method may include administering to a subject in need of such treatment a composition including a therapeutically effective amount of an agent that mediates upregulation of Transcription Factor EB (TFEB).
  • TFEB Transcription Factor EB
  • the agent is a statin.
  • the statin may be atorvastatin, fluvastatin, lovastatin, pitavastatin, pravastatin, rosuvastatin, or simvastatin.
  • the agent may also be, for example, a lipid-lowering drug, such as a fibrate.
  • the fibrate is gemfibrozil or fenofibrate.
  • the agent is an analgesic, an antipyretic, aspirin, a cinnamon metabolite, cinnamic acid, sodium phenylbutyrate or sodium benzoate.
  • the composition may include a combination of at least two of the above agents.
  • the composition may also include all-trans retinoic acid or vitamin A.
  • the composition may include a statin or a fibrate and all-trans retinoic acid or vitamin A.
  • This combination of the agent(s) with all-trans retinoic acid or vitamin A may provide a greater therapeutic effect in the subject than administration of the all-trans retinoic acid, vitamin A or the fibrate alone.
  • the combination may be a synergistic combination.
  • TFEB may also be upregulated by increasing Transcription Factor EB mRNA levels increasing Transcription Factor EB protein levels or activating a PPAR ⁇ -RXR ⁇ heterodimer.
  • the LSD may be a neurodegenerative disorder, for example, neuronal ceroid lipofuscinosis, Alzheimer's disease, Huntington's disease, Amyotrophic lateral sclerosis (ALS), Parkinson's disease, including Parkinson's plus diseases such as multiple system atrophy (MSA), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD) or dementia with Lewy bodies (DLB).
  • the LSD is a disorder of the autophagy pathway and wherein the agent increases lysosomal biogensis.
  • the LSD is Tay-Sach's disease, Fabry disease, Niemann-Pick disease, Gaucher disease, Hunter Syndrome, Alpha-mannosidosis, Aspartylglucosaminuria, Cholesteryl ester storage disease, Chronic Hexosaminidase A Deficiency, Cystinosis, Danon disease, Farber disease, Fucosidosis, Galactosialidosis, or Batten disease including late infantile Batten disease and Juvenile Batten disease.
  • Another aspect of the present invention provides a method for treatment of a LSD including administering to a subject in need of such treatment a composition including a therapeutically effective amount of an agent that mediates upregulation of the Tfeb gene. Yet another aspect provides a method for treatment of a LSD including administering to a subject in need of such treatment a composition including a therapeutically effective amount of an agent, wherein the agent restores TFEB activity.
  • FIG. 1 shows Gemfibrozil and Retinoic Acid upregulating TFEB mRNA and protein levels in brain cells.
  • A, B Mouse primary astrocytes were treated with different concentrations of gemfibrozil and all-trans retinoic acid (ATRA) under serum free DMEM/F-12 medium for 12 hrs followed by monitoring mRNA levels of Tfeb by qRT-PCR (A) and TFEB protein levels by immunoblot (B).
  • A gemfibrozil and all-trans retinoic acid
  • G, I Mouse primary astrocytes (G) and mouse primary neurons (I) were treated with combination of gemfibrozil and retinoic acid under serum free condition for 24 hrs and were double labeled for TFEB (red)-GFAP (green) and TFEB (red)-Map2 (green), respectively.
  • TFEB IR TFEB immunoreactivity
  • FIG. 2 shows involvement of PPAR ⁇ and RXR ⁇ in fibrate drug-mediated upregulation of TFEB mRNA and protein:
  • A, B Mouse primary astrocytes isolated from PPAR ⁇ / ⁇ and PPAR ⁇ / ⁇ and wild type mouse were treated with combination of gemfibrozil (10 ⁇ M) and retinoic acid (0.2 ⁇ M) in serum free DMEM/F12 for 24 hrs followed by monitoring the mRNA expression of Tfeb by real-time PCR (A) and protein level of TFEB by immunoblot (B).
  • A real-time PCR
  • B protein level of TFEB by immunoblot
  • C Densitometric analysis of TFEB levels (relative to ⁇ -Actin) in PPAR ⁇ / ⁇ and PPAR ⁇ / ⁇ and wild type astrocytes.
  • H, I, J Mouse primary astrocytes were untransfected, transfected with scrambled siRNA (1.0 ⁇ g) or RXR ⁇ siRNA (1.0 ⁇ g) for 36 hrs followed by treatment with RA (0.2 ⁇ M) and gemfibrozil (10 ⁇ M) in combination for 24 hrs serum free DMEM/F12 medium followed by RT-PCR for RXR ⁇ to check the level of gene silencing (H) and quantitative real time PCR for TFEB (J) and immunoblot for TFEB (J).
  • FIG. 3 shows PPAR ⁇ transcriptionally regulating TFEB expression under treatment condition:
  • A Map of wild-type and mutated PPRE site of TFEB-Luciferase promoter constructs.
  • B BV2 cells were transfected with pTFEB(WT)-Luc for 24 hrs followed by treatment with different concentrations of gemfibrozil and retinoic acid alone and in combination and subjected to luciferase assay. p* ⁇ 0.05 vs untreated control.
  • (C) BV2 cells were transfected with pTFEB(WT)-Luc for 24 hrs followed by pretreatment with PPAR ⁇ -, PPAR ⁇ -, PPAR ⁇ -antagonists followed by treatment with gemfibrozil and retinoic acid and subjected to luciferase assay. p* ⁇ 0.05 vs untreated control. p# ⁇ 0.05 vs treatment.
  • FIG. 4 shows trancriptional activation of TFEB by PPAR ⁇ -RXR ⁇ -PGC1 ⁇ complex
  • A Map of PPRE on TFEB promoter with core sequence and amplicon length for ChIP.
  • B,C Mouse astrocytes were treated with the combination of gemfibrozil (10 ⁇ M) and RA (0.2 ⁇ M) for 30, 60, 120 and 240 mins and recruitment of PPAR ⁇ (far left), RXR ⁇ (center left), PGC1 ⁇ (center right) and RNA Polymerase (far right) on the PPRE binding site of Tfeb promoter was monitored by ChIP followed by RT-PCR (B) and qRT-PCR (C). Normal IgG was used as control. p* ⁇ 0.05 vs untreated control. All results are representative of or mean ⁇ SEM at least there independent sets of experiments.
  • D Schematic representation of induction of lysosomal biogenesis by activating peroxisomal proliferators.
  • FIG. 5 shows PPAR ⁇ dependant upregulation of TFEB inducing lysosomal biogenesis:
  • A, B Mouse primary astrocytes isolated from PPAR ⁇ / ⁇ and PPAR ⁇ / ⁇ and wild type mouse were treated with combination of gemfibrozil (10 ⁇ M) and retinoic acid (0.2 ⁇ M) in serum free DMEM/F12 for 24 hrs followed by monitoring the mRNA expression of lysosomal genes (Lamp2 (left), Limp2 (center), Npc1(right)) by real-time PCR (A) and protein level of LAMP2 by immunoblot (B).
  • gemfibrozil 10 ⁇ M
  • retinoic acid 0.2 ⁇ M
  • C, F, I Higher magnification images showing localization of TFEB and NeuN in the cortical neuron of mice from the treatment group (WT, PPAR ⁇ / ⁇ and PPAR ⁇ / ⁇ ).
  • C, F, I Higher magnification images showing localization of LAMP2 and NeuN in the cortical neuron of mice from the treatment group (WT, PPAR ⁇ / ⁇ and PPAR ⁇ / ⁇ ).
  • FIGS. 9(A)-9(D) illustrate the upregulation of TFEB mRNA expression in mouse astrocytes by cholesterol-lowering drugs (simvastatin and pravastatin), aspirin (anasgesic and anti-pyretic), cinnamic acid (metabolite of cinnamon), and drugs for urea cycle disorders (sodium phenylbutyrate and sodium benzoate).
  • FIG. 10 illustrates an increase in lysosomal biogenesis by aspirin in primary mouse astrocytes.
  • Cells were treated with different concentrations of aspirin for 24 h under serum-free condition followed by Lyso-tracker staining. Results represent three independent experiments.
  • FIG. 11(A) -(D) shows the upregulation of LAMP2 expression by aspirin in primary mouse astrocytes.
  • 11 (A) Cells were treated with 5 ⁇ M aspirin for different time periods under serum-free condition followed by monitoring the mRNA expression of LAMP2 by real-time PCR. Results are mean+SD of three different experiments. ap ⁇ 0.05 vs control; bp ⁇ 0.001 vs control.
  • 11 (B) Cells were treated with different concentrations of aspirin for 24 h under serum-free condition followed by Western blot for LAMP2.
  • 11 (C) Cells were treated with 5 ⁇ M aspirin for different time periods under serum-free condition followed by Western blot for LAMP2.
  • 11 (D) After 24 h of aspirin treatment, cells were double-labeled for LAMP2 and GFAP. Results represent three independent experiments.
  • FIG. 12(A) -(C) shows an increase in TPP1 by aspirin in primary mouse astrocytes.
  • 12 (A) Cells were treated with different concentrations of aspirin for 24 h under serum-free condition followed by Western blot for TPP1.
  • FIG. 13(A) -(C) illustrates the upregulation of TFEB by aspirin in primary mouse astrocytes.
  • 13 (A) Cells were treated with different concentrations of aspirin for 12 h under serum-free condition followed by Western blot for TFEB. Actin was run as a house keeping molecule.
  • 13 (B) Cells were treated with 5 ⁇ M aspirin for 12 h under serum-free condition followed by double-labeling with GFAP and TFEB. These results are mean of two independent experiments.
  • 13 (C) Cells were transfected with p(WT)Tfeb-Luc plasmid and after 24 h of transfection, cells were stimulated with different doses of aspirin. After 4 h, firefly luciferase activity was measured in total cell extracts. Results are mean+SD of three different experiments. a p ⁇ 0.001 vs control.
  • FIG. 14(A) -(B) illustrates activation of PPAR ⁇ by aspirin in primary mouse astrocytes.
  • 14 (A) Cells were treated with 5 ⁇ M aspirin for different min intervals followed by isolation of nuclear extracts and electrophoretic mobility shift assay for monitoring DNA-binding activity of PPAR ⁇ using PPAR ⁇ -binding site of the Tfeb promoter as a probe.
  • 14 (B) Astrocytes isolated from wild type, PPAR ⁇ ( ⁇ / ⁇ ) and PPAR ⁇ ( ⁇ / ⁇ ) mice were transfected with PPAR luciferase reporter (PPRE-x3-TK-luc) plasmid and after 24 h of transfection, cells were stimulated with different doses of aspirin. After 4 h, firefly luciferase activity was measured in total cell extracts. Results are mean+SD of three different experiments. a p ⁇ 0.001 vs control.
  • FIG. 15(A) -(C) illustrates that aspirin increases the level of TFEB in astrocytes via PPAR ⁇ .
  • Astrocytes isolated from WT 15 (A), PPAR ⁇ ( ⁇ / ⁇ ) 15 (B) and PPAR ⁇ ( ⁇ / ⁇ ) 15 (C) mice were treated with 5 ⁇ M aspirin for 12 h under serum-free condition followed by double-labeling for TFEB and GFAP. Results represent three independent experiments.
  • FIG. 16(A) -(B) illustrates that aspirin increases the level of LAMP2 in astrocytes via PPAR ⁇ .
  • Astrocytes isolated from WT, PPAR ⁇ ( ⁇ / ⁇ ) and PPAR ⁇ ( ⁇ / ⁇ ) mice were treated with different concentrations of aspirin for 24 h under serum-free condition followed by Western blot analysis for LAMP2 16 (A). Actin was run as a house keeping molecule. Bands were scanned and expressed as relative to control 16 (B). Results are mean+SD of three different experiments. a p ⁇ 0.05 vs control; b p ⁇ 0.001 vs control. ns, not significant.
  • FIGS. 17(A) -(C) illustrate that aspirin increases lysosomal biogenesis in astrocytes via PPAR ⁇ .
  • Astrocytes isolated from WT 17 (A), PPAR ⁇ ( ⁇ / ⁇ ) 17 (B) and PPAR ⁇ ( ⁇ / ⁇ ) 17 (C) mice were treated with 5 ⁇ M aspirin for 24 h under serum-free condition followed by Lyso-tracker staining. Results represent three independent experiments.
  • the term subject refers to a human or veterinary subject.
  • therapeutic effect means an effect which induces, ameliorates or otherwise causes an improvement in the pathological symptoms, disease progression or physiological conditions associated with or resistance to succumbing to a disorder, for example a LSD, of a subject.
  • therapeutically effective amount as used with respect to a drug means an amount of the drug which imparts a therapeutic effect to the subject.
  • synergy mean more than the expected additive effect of a combination.
  • a synergistic effect may be attained when the active ingredients are: (1) co-formulated and administered or delivered simultaneously in a combined, unit dosage formulation; (2) delivered by alternation or in parallel as separate formulations; or (3) by some other regimen.
  • LSD lysosomal storage disorder
  • the LSD may be, for example, Tay-Sach's disease, Fabry disease, Niemann-Pick disease, Gaucher disease, Hunter Syndrome, Alpha-mannosidosis, Aspartylglucosaminuria, Cholesteryl ester storage disease, Chronic Hexosaminidase A Deficiency, Cystinosis, Danon disease, Farber disease, Fucosidosis, Galactosialidosis or Batten disease including late infantile Batten disease and Juvenile Batten disease.
  • the LSD may also be a neurodegenerative disease involving the autophagy-lysosome pathway, for example, neuronal ceroid lipofuscinosis, Alzheimer's disease, Huntington's disease, Amyotrophic lateral sclerosis (ALS), Parkinson's disease, including Parkinson's plus diseases such as multiple system atrophy (MSA), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD) or dementia with Lewy bodies (DLB).
  • the neurodegenerative disorder may be characterized by defective autophage. Such disorders include Alzheimer's, Parkinson's disease, and Huntington's disease.
  • One embodiment includes administering to a subject suffering from a LSD an agent that upregulates or enhances expression from the Tfeb gene.
  • Upregulation may include increasing mRNA levels for Tfeb.
  • the methods of the present invention also include administering to a subject suffering from a LSD an agent that upregulates TFEB or restores TFEB activity.
  • Upregulation may include increasing TFEB mRNA levels, increasing TFEB protein levels, or increasing TFEB activity.
  • Activating a PPAR ⁇ /RXR ⁇ heterodimer results in upregulation of TFEB.
  • the inventor has also surprisingly shown that TFEB is upregulated through the activity or involvement of PPAR ⁇ , but not PPAR ⁇ or PPAR ⁇ .
  • the agent may be a lipid-lowering drug such as a fibrate.
  • the fibrate may be gemfibrozil, fenofibrate, or clofibrate.
  • the agent may be all-trans retinoic acid or vitamin A.
  • administration of the fibrate in combination with all-trans retinoic acid or vitamin A to the subject may upregulate TFEB more than administration of the fibrate or all-trans retinoic acid or vitamin A alone.
  • the fibrate and all-trans retinoic acid or vitamin A when administered together to the subject, may cooperatively enhance upregulation of TFEB to synergistically upregulate TFEB.
  • a lower dose of the fibrate may be needed in the presence of all-trans retinoic acid or vitamin A to achieve the same degree of TFEB upregulation as occurs when only a higher dose of the fibrate is administered to the subject.
  • the combination of the fibrate and all-trans retinoic acid or vitamin A may be a synergistic combination.
  • the lipid lowering drug is a statin.
  • the statin may be atorvastatin, fluvastatin, lovastatin, pitavastatin, pravastatin, rosuvastatin, simvastatin or a combination of at least two of these drugs.
  • the statin or statins may be used alone or in combination with a fibrate and or all-trans retinoic acid or vitamin A.
  • the agent may be an analgesic or antipyretic, for example aspirin; phenylbutyrate; sodium benzoate; or a cinnamon metabolite, for example cinnamic acid.
  • such agents may be used in combination with all-trans retinoic acid or vitamin A and may be administered together to the subject to cooperatively enhance upregulation of TFEB to synergistically upregulate TFEB.
  • the lipid lowering drugs may be drugs that reduce the level of triglycerides circulating in the blood of the subject. Additionally, lipid-lowering drugs may be drugs that decrease the risk of hyperlipidemia.
  • the fibrate may mediate upregulation of TFEB via PPAR ⁇ , but not PPAR ⁇ and PPAR ⁇ . During upregulation of TFEB, PPAR ⁇ forms a heterodimer with RXR- ⁇ and the RXR ⁇ /PPAR-a heterodimer is recruited to the promoter of the Tfeb gene via a RXR binding site.
  • the upregulation of TFEB may also be mediated by all-trans retinoic acid. All-trans retinoic acid may also be known as ATRA, retinoic acid, tretinoin, and vitamin A acid. All-trans retinoic acid may mediate upregulation of TFEB via the retinoid X receptor- ⁇ (RXR- ⁇ ). During upregulation of TFEB, RXR- ⁇ forms a heterodimer with peroxisome proliferator-activated receptor-a (PPAR- ⁇ ) and the RXR- ⁇ /PPAR- ⁇ heterodimer is recruited to the promoter of the Tfeb gene via a RXR binding site.
  • All-trans retinoic acid may also be known as ATRA, retinoic acid, tretinoin, and vitamin A acid. All-trans retinoic acid may mediate upregulation of TFEB via the retinoid X receptor- ⁇ (RXR- ⁇ ).
  • RXR- ⁇ forms a heterodi
  • the composition mediating upregulation of TFEB may include a combination of the agent, for example, a lipid lowering drug, and all-trans retinoic acid or vitamin A.
  • a combination may cooperatively mediate or enhance upregulation of TFEB as compared to administration of the agent or all-trans retinoic acid or vitamin A alone.
  • the combination may cooperatively enhance upregulation of TFEB about 2-fold, about 3-fold, about 4-fold, about 5-fold, or about 10-fold as compared to administration of the lipid-lowering drug or all-trans retinoic acid or vitamin A alone.
  • the combination may cooperatively enhance upregulation of TFEB about 3-fold as compared to administration of the lipid-lowering drug or all-trans retinoic acid or vitamin A alone.
  • compositions including at least one of the agents disclosed above.
  • the pharmaceutical composition may also include all-trans retinoic acid or vitamin A.
  • the pharmaceutical composition may include gemfibrozil or a combination of gemfibrozil and all-trans retinoic acid or vitamin A or a combination of aspirin and all-trans retinoic acid or vitamin A.
  • compositions can be in the form of, for example, tablets, pills, dragees, hard and soft gel capsules, granules, pellets, aqueous, lipid, oily or other solutions, emulsions such as oil-in-water emulsions, liposomes, aqueous or oily suspensions, syrups, alixiers, solid emulsions, solid dispersions or dispersible powders.
  • the agent may be admixed with commonly known and used adjuvants and excipients, for example, gum arabic, talcum, starch, sugars (such as, e.g., mannitose, methyl cellulose, lactose), gelatin, surface-active agents, magnesium stearate, aqueous or non-aqueous solvents, paraffin derivatives, cross-linking agents, dispersants, emulsifiers, lubricants, conserving agents, flavoring agents (e.g., ethereal oils), solubility enhancers (e.g., benzyl benzoate or benzyl alcohol) or bioavailability enhancers (e.g. GELUCIRE).
  • the agent may also be dispersed in a microparticle, e.g. a nanoparticulate, composition.
  • the agent or pharmaceutical compositions of the agent can be dissolved or suspended in a physiologically acceptable diluent, such as, e.g., water, buffer, oils with or without solubilizers, surface-active agents, dispersants or emulsifiers.
  • a physiologically acceptable diluent such as, e.g., water, buffer, oils with or without solubilizers, surface-active agents, dispersants or emulsifiers.
  • oils for example and without limitation, olive oil, peanut oil, cottonseed oil, soybean oil, castor oil and sesame oil may be used.
  • the agent or pharmaceutical compositions of the agent can be in the form of an aqueous, lipid, oily or other kind of solution or suspension or even administered in the form of liposomes or nano-suspensions.
  • the agents disclosed above or pharmaceutical compositions including these agents can be administered by any method that allows for the delivery of a therapeutic effective amount of the agent to the subject.
  • Modes of administration can include, but are not limited to, oral, topical, transdermal and parenteral routes, as well as direct injection into a tissue, and delivery by a catheter.
  • Parenteral routes can include, but are not limited to subcutaneous, intradermal, intra-articular, intravenous, intraperitoneal and intramuscular routes.
  • the route of administration is by topical or transdermal administration, such as by a lotion, cream, a patch, an injection, an implanted device, a graft or other controlled release carrier.
  • Routes of administration include any route which directly delivers the composition to the systemic circulation (e.g., by injection), including any parenteral route.
  • One embodiment of the method of the present invention comprises administering at least one agent, for example gemfibrozil or a combination of gemfibrozil and ATRA, in a dose, concentration and for a time sufficient to prevent the development of, or to lessen the extent of, a LSD.
  • Certain embodiments include administering systemically at least one agent in a dose between about 0.1 micrograms and about 100 milligrams per kilogram body weight of the subject, between about 0.1 micrograms and about 10 milligrams per kilogram body weight of the subject, between about 0.1 micrograms and about 1 milligram per kilogram body weight of the subject.
  • the agent or therapeutic composition containing the agent can be administered in a single daily dose or in multiple doses per day. This treatment method may require administration over extended periods of time.
  • the amount per administered dose or the total amount administered will be determined by the physician and will depend on such factors as the mass of the patient, the age and general health of the patient and the tolerance of the patient to the compound.
  • DMEM/F-12 50/50 1 ⁇ , Hank's balanced salt solution (HBSS) and 0.05% trypsin were purchased from Mediatech (Washington, D.C.).
  • Fetal bovine serum (FBS) was obtained from Atlas Biologicals (Fort Collins, Colo.).
  • Antibioticantimycotic, gemfibrozil and all trans retinoic acid (ATRA) were obtained from Sigma-Aldrich (St. Louis, Mo.).
  • Astroglia were isolated from mixed glial cultures as described (24, 25) according to the procedure of Giulian and Baker (26). Briefly, on day 9, the mixed glial cultures were washed three times with Dulbecco's modified Eagle's medium/F-12 and subjected to shaking at 240 rpm for 2 h at 37° C. on a rotary shaker to remove microglia. After 2 days, the shaking was repeated for 24 h for the removal of oligodendroglia and to ensure the complete removal of all nonastroglial cells. The attached cells were seeded onto new plates for further studies.
  • Fetal (E18-E16) mouse neurons were prepared as previously described (27) with modifications. Whole brains were removed and the cells were washed by centrifugation three times at 1200 rpm for 10 min, the pellet dissociated and the cells plated at 10% confluence in 8-well chamber slides pre-treated for >2 hr with Poly-D-Lysine (Sigma, St. Louis, Mo.). After 4 min, the non-adherent cell suspension was aspirated and 500 ml complete Neurobasal media (Invitrogen) supplemented with 2% B27 was added to each well. The cells were incubated for 4 days prior to experimentation.
  • Neurobasal media Invitrogen
  • Double-label immunofluorescence with ⁇ -tubulin and either GFAP or CD11b revealed that neurons were more than 98% pure (data not shown).
  • the cells were stimulated with gemfibrozil in Neurobasal media supplemented with 2% B27 minus antioxidants (Invitrogen) for 24 hr prior to methanol fixation and immunostaining.
  • RT-PCR Semi-Quantitative Reverse Transcriptase-Coupled Polymerase Chain Reaction
  • Mouse Tfeb Sense, (SEQ ID NO.: 1) 5′-AAC AAA GGC ACC ATC CTC AA-3′; Antisense, (SEQ ID NO.: 2) 5′-CAG CTC GGC CAT ATT CAC AC-3′; Mouse Lamp2: Sense, (SEQ ID NO.: 3) 5′-GGT GCT GGT CTT TCA GGC TTG ATT-3′; Antisense, (SEQ ID NO.: 4) 5′-ACC ACC CAA TCT AAG AGC AGG ACT-3′; Mouse Limp2: Sense, (SEQ ID NO.: 5) 5′-TGT TGA AAC GGG AGA CAT CA-3′; Antisense, (SEQ ID NO.: 6) 5′-TGG TGA CAA CCA AAG TCG TG-3′; Mouse Npc1: Sense, (SEQ ID NO.: 7) 5′-GGG ATG CCC GTG CCT GCA AT-3′; Antisense, (SEQ ID NO.
  • Amplified products were electrophoresed on 2% agarose (Invitrogen) gels and visualized by ethidium bromide (Invitrogen) staining.
  • Glyceraldehyde-3-phosphate dehydrogenase (Gapdh) mRNA was used as a loading control to ascertain that an equivalent amount of cDNA was synthesized from each sample.
  • the mRNA quantification was performed using the ABIPrism7700 sequence detection system (Applied Biosystems, Foster City, Calif.) using SYBR Select master mix (Applied Biosystems).
  • the mRNA expression of the targeted genes was normalized to the level of Gapdh mRNA and data was processed by the ABI Sequence Detection System 1.6 software.
  • Immunocytochemistry was performed as described earlier (29). Briefly, 8 well chamber slides containing mouse primary astrocytes, mouse neurons were cultured to 70-80% confluence were fixed with chilled Methanol (Fisher Scientific, Waltham, Mass.) overnight, followed by two brief rinses with filtered PBS.
  • DAPI 4′,6-diamidino-2-phenylindole
  • mice After 60 days of treatment, mice were sacrificed and their brains fixed, embedded, and processed. Sections were made from different brain regions and for immunofluorescence staining on fresh frozen sections, anti-mouse TFEB (1:500), anti-mouse LAMP2 (1:200) and anti-mouse NeuN (1:500) were used. The samples were mounted and observed under Olympus BX41 fluorescence microscope (30).
  • Fibroblasts cultured to 70-80% confluence were subjected to different stimuli under reduced serum (2%) DMEM medium followed by incubation with 75 nM LysoTracker Red DND99 (Invitrogen) for 45 mins. Cells were then washed thoroughly with filtered PBS and mounted on glass slides and viewed under BX41 fluorescence microscope
  • membranes were then washed for 15 min in TBS plus Tween 20 (TBST) and blocked for 1 hr in TBST containing BSA. Next, membranes were incubated overnight at 4° C. under shaking conditions with the following 1° antibodies; TFEB (1:1000, Abcam), LAMP2 (1:500, Abcam) and ⁇ -actin (1:800; Abcam, Cambridge, Mass.). The next day, membranes were washed in TBST for 1 hr, incubated in 2° antibodies against 1° antibody hosts (all 1:10,000; Jackson ImmunoResearch) for 1 hr at room temperature, washed for one more hour and visualized under the Odyssey® Infrared Imaging System (Li-COR, Lincoln, Nebr.).
  • Mouse genomic DNA isolated from primary mouse astrocytes was used as the template during PCR.
  • the 5′ flanking sequence of the mouse TFEB ( ⁇ 916/+61) gene was isolated by PCR.
  • Primers were designed from gene bank sequences.
  • Tfeb sense: 5′-acgcgt CCA GGA GCC AGG GAC GGG GTA CAT CTC-3′ (SEQ ID NO.: 11); antisense: 5′-agatct AAG GAG AAA CTG AGT CCG GGC AGA AGG-3′ (SEQ ID NO.: 12).
  • the sense primer was tagged with an Mlu1 restriction enzyme site while the antisense primer was tagged with Bgl II.
  • the PCR was performed using an Advantage-2 PCR kit (Clontech) according to the manufacturer's instruction.
  • the resulting fragments were gel purified and ligated into the PGEM-TEasy vector (Promega). These fragments were further subcloned into the PGL-3 Enhancer vector after digestion with corresponding restriction enzymes and verification by sequencing ACGT Inc. DNA Sequencing Services.
  • Site-directed mutagenesis was done by using the site directed mutagenesis kit (Stratagene, USA). Two primers in opposite orientation were used to amplify the mutated plasmid in a single PCR reaction.
  • the primer sequence for mutated promoter site were: Mutated: Sense: 5′-GCA ACA GCA AGT GCG GAT TTG AGG GGG GGG GAC GGT GGG-3′ (SEQ ID NO.: 13); Antisense: 5′-CCC ACC GTC CCC CCC CCT CAA ATC CGC ACT TGC TGT TGC-3′ (SEQ ID NO.: 14).
  • the PCR product was precipitated with ethanol and then phosphorylated by T4 kinase.
  • the phosphorylated fragment was self-ligated by T4 DNA ligase and digested with restriction enzyme DpnI to eliminate the non-mutated template.
  • the mutated plasmid was cloned and amplified in Escherichia coli (DH5- ⁇ strain) competent cells.
  • ChIP assays were performed using method described by Nelson et al (35), with certain modifications. Briefly, mouse primary astrocytes were stimulated by 10 ⁇ M gemfibrozil and 0.5 ⁇ M RA together for 6 hrs followed by fixing with formaldehyde (1.42% final volume) and quenching with 125 mM Glycine. The cells were pelleted and lysed in IP buffer containing 150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, NP-40 (0.5% vol/vol), Triton X-100 (1.0% vol/vol).
  • Chelex/protein G bead suspension was allowed to cool to room temperature. Proteinase K (100 ⁇ g/ml) was then added and beads were incubated for 30 min at 55° C. while shaking, followed by another round of boiling for 10 min. The suspension was centrifuged and supernatant collected. The Chelex/protein G beads fraction was vortexed with another 100 ⁇ l water, centrifuged again, and the first and the second supernatants were combined. Eluate was used directly as a template in PCR.
  • the following primers were used to amplify fragments flanking RXR binding element in the mouse Tfeb promoter: Set1: sense: 5′-GAA CAT TCC AGG TGG AGG CA-3′ (SEQ ID NO.: 15), antisense: 5′-CCC CCA ACA CAT GCT TCT CT-3′ (SEQ ID NO.: 16); Set2: sense: 5′-GAG TCT CTC GGA GGA GGT GA-3′ (SEQ ID NO.: 17), antisense: 5′-ACT CCA GGC ATG CTT TCT CC-3′(SEQ ID NO.: 18).
  • the PCRs were repeated by using varying cycle numbers and different amounts of templates to ensure that results were in the linear range of PCR.
  • the qRT-PCR was performed using the same primers and SYBR select mastermix. Data were normalized to input and non-specific IgG and fold increase vs control was calculated.
  • Protein blots were analyzed using ImageJ (NIH, Bethesda, Md.) and bands were normalized to their respective ⁇ -actin loading controls. Data are representative of the average fold change with respect to control for at least 25 different images per condition from three independent set of experiments.
  • PPAR activators like the FDA-approved drug gemfibrozil, where examined to determine if they could upregulate the expression of TFEB in mouse brain cells. Since it has been known that PPAR ⁇ and RXR ⁇ forms a transcriptionally active complex (21, 36, 37), we used both gemfibrozil and ATRA, which activates RXR ⁇ , to check if there is any additive effect due to dual treatment.
  • Mouse primary astrocytes (MPA) were treated in serum free media with single doses of gemfibrozil and ATRA and also in combination. Quantitative realtime PCR data showed increased expression of Tfeb in all three groups with the increase being marginally higher in combinatorial treatment (but not statistically significant w.r.t individual treatments) ( FIG. 1A ).
  • FIGS. 1G & 1I The TFEB immunoreactivity was quantified using ImageJ and we observed ⁇ 4-fold increase in the overall levels of TFEB and ⁇ 5-6-fold increase of TFEB localization of TFEB in the nucleus upon treatment ( FIGS.
  • Example 3 PPAR ⁇ and RXR ⁇ are Involved in the Drug Mediated Upregulation of TFEB
  • PPAR ⁇ coactivator-1a (PGC1A) could be involved in transcriptionally activating Tfeb, so we tested whether PPAR ⁇ is involved in this particular drug mediated expression of TFEB by using PPAR ⁇ inhibitors.
  • Western blot for TFEB using pretreatment with PPAR ⁇ specific inhibitors prior to treatment with the drugs indicate that gemfibrozil and ATRA may not be using the PPAR ⁇ mediated pathway for the upregulation of TFEB ( FIGS. 2D & 2E ).
  • PPAR ⁇ and RXR ⁇ have been known to form a transcriptional complex and our data showed marginal increase of TFEB in presence of ATRA. We wanted to see whether ATRA exerts its effects via RXR ⁇ .
  • WT MPAs were treated with RXR ⁇ specific siRNA followed by treatment with the combination of gemfibrozil and ATRA and both mRNA and protein analyses were performed.
  • the data showed a successful knockdown of RXR ⁇ gene and consequently the effect of drugs were partially abrogated in absence of RXR ⁇ , which was evident from the levels of Tfeb mRNA after RXR ⁇ silencing ( FIGS. 2H & 2I ).
  • the western blot also showed similar results with the TEFB levels being significantly less in RXR ⁇ silenced cells compared to scrambled siRNA after treatment ( FIGS. 2J & 2K ). Taken together these data indicate that PPAR ⁇ and RXR ⁇ could be involved in the upregulation of TFEB by gemfibrozil and ATRA.
  • PPAR ⁇ and RXR ⁇ together form a transcriptional complex, so having determined that those receptors appear to upregulate Tfeb, we tested whether the receptors transcriptionally regulate Tfeb expression.
  • Tfeb Peroxisomal Proliferator Response Element
  • pTFEB(WT) The Tfeb promoter containing the PERO was cloned into the pGL3 Enhancer vector.
  • pTFEB(Mu) was also cloned into PGL3 vector.
  • the Wild type luciferase construct when transfected into BV2 cells showed marked increase in the luciferase activity ( FIG. 3B ).
  • the cells containing the pTFEB(WT) luciferase construct were treated with PPAR ⁇ -antagonist (GW6471; 250 nM), PPAR ⁇ -antagonist (GSK0660; 250 nM), PPAR ⁇ -antagonist (GW9662; 5 nM) we observed the luciferase activity was similar to the untreated cells in PPAR ⁇ antagonist treated cells, but not in the PPAR ⁇ - or PPAR ⁇ -antagonist treated cells ( FIG. 3C ).
  • TFEB is the master regulator of lysosomal gene expression and biogenesis (9,12,16) so we expected an increase in the biogenesis and lysosomal markers with the upregulation of TFEB.
  • the MPAs treated under the same condition were subjected to mRNA analysis for some lysosomal markers like Lamp2, Limp2 and Npc1. As expected the data showed elevated levels of those genes under treatment conditions in WT and PPAR ⁇ ( ⁇ / ⁇ ) cells, but not in PPAR ⁇ ( ⁇ / ⁇ ) cells.
  • FIG. 5A Western blot analysis and immunocytochemistry for LAMP2 in WT and K.O. cells showed a similar protein expression pattern as well ( FIGS. 5B, 5C & 5D ).
  • Example 6 Agonists of PPAR ⁇ and RXR ⁇ Induce Lysosomal Biogenesis In Vivo in the CNS of WT and PPAR ⁇ / ⁇ , but not in PPAR ⁇ / ⁇ , Mice
  • Example 8 Discussion of Examples 2 to 7
  • Lysosomes are one of the major organelles in cells that not only act as the waste management machinery of the cell but also play significant roles in other biological processes like antigen presentation, regulation of certain hormones, bone remodeling, necrotic cell death, cell surface repair, and developmental and other signaling pathways (2, 43-47). In order to carry out these varied functions the biogenesis and activity of lysosomes needs to be tightly regulated. According to recent findings, TFEB is a master regulator of lysosomal biogenesis (9, 12, 15). Over the years different groups have underscored the role of lysosome in different disease scenarios (48-53).
  • Lysosome-related genes are reported to be closely regulated in the orbital fat of patients suffering from Graves' ophthalmopathy whereas down-regulation of lysosomal processing improved pegylated lipopolyplex-mediated gene transfection (53, 54).
  • the increase in lysosomal biogenesis may not necessarily prove to be beneficial in all disease and cell types, but in some cases induction of the autophagy-lysosomal pathway could be helpful for cellular clearance of toxic wastes (55, 56).
  • TFEB transcription factor EB
  • TFEB was shown to rescue the activity of a ⁇ -hexosaminidase mutant.
  • the findings describe TFEB as specific regulator of lysosomal proteostasis and a therapeutic target to rescue enzyme homeostasis in LSDs (60,61).
  • TFEB has become a potentially important transcription factor for its role in not only lysosomal biogenesis but also due to its implications as a therapeutic target in disease conditions.
  • PPAR ⁇ has been shown to play significant role in different regulatory and modulatory pathways (67-71).
  • Certain polyunsaturated fatty acids and oxidized derivatives and by lipid-modifying drugs of the fibrate family, including fenofibrate and gemfibrozil has been known to activate PPAR ⁇ .
  • Fibrate drugs replace the HSP90 repressor complex which sequesters PPAR ⁇ in the cytosol and help to rescue the transcriptional activity of PPAR ⁇ (21). Therefore, we assessed the role of the PPAR group of receptors for this phenomenon.
  • Our data clearly indicate the involvement of PPAR ⁇ , but not PPAR ⁇ and PPAR ⁇ , in the process of upregulation of TFEB by gemfibrozil.
  • the in vitro studies were further validated by in vivo studies, in which we used the knockout mice for PPAR ⁇ and PPAR ⁇ . Our in vivo results also supported the cell culture data.
  • the luciferase assay results using both WT and mutant luciferase construct of the PERO on the Tfeb promoter showed increased Tfeb promoter dependant activity in the WT construct upon stimulation.
  • PPAR ⁇ ( ⁇ / ⁇ ) cells when transfected with pTFEB(WT)-Luc construct and also WT cells when transfected with pTFEB(Mu)-Luc construct did not show any significant increase in the luciferase activity.
  • the ChIP data indicated the recruitment of the PPAR ⁇ and RXR ⁇ along with PGC1 ⁇ and RNA Pol on the PERO site of the TFEB promoter. The experimental data was critically analyzed along with incorporation of proper controls to ensure the specificity of the findings.
  • FIG. 9 illustrates the upregulation of TFEB mRNA expression in mouse astrocytes by cholesterol-lowering drugs (simvastatin and pravastatin), aspirin (anasgesic and anti-pyretic), cinnamic acid (metabolite of cinnamon), and drugs for urea cycle disorders (sodium phenylbutyrate and sodium benzoate).
  • Mouse primary astrocytes were incubated with different concentrations (see FIG. 9 ) of simvastatin and pravastatin (A), (B), cinnamic acid (C), and sodium phenylbutyrate and sodium benzoate (D) for 5 hr. under serum-free condition followed by monitoring the mRNA expression of TFEB by semi-quantitative RT-PCR.
  • Sodium formate (D) was used as a negative control for sodium phenylbutyrate and sodium benzoate.
  • LAMP2 is an important lysosomal membrane protein, which plays a key role in the formation of new lysosomes.
  • FIG. 11A time-dependent increase in LAMP2 mRNA
  • FIG. 11C protein expression by aspirin in astrocytes.
  • FIG. 11B LAMP2 increase by aspirin was further confirmed by immunostaining.
  • TPP1 Tripeptidylpeptidase 1
  • astrocytes Tripeptidylpeptidase 1
  • FIG. 12A Increase in TPP1 protein in response to 5 ⁇ M aspirin was evident as early as 2 h, which was maximum at 12 h of incubation ( FIG. 12B ).
  • FIG. 12C we observed increase in TPP1 activity at 2 and 5 ⁇ M, but not 10 ⁇ M, aspirin ( FIG. 12C ).
  • TFEB is a master regulator of lysosomal biogenesis (9, 12, 25).
  • Lysosome-related genes are reported to be closely regulated in the orbital fat of patients suffering from Graves' ophthalmopathy whereas down-regulation of lysosomal processing improved pegylated lipopolyplex-mediated gene transfection (53, 54).
  • the increase in lysosomal biogenesis may not necessarily prove to be beneficial in all disease and cell types, but in some cases induction of the autophagy-lysosomal pathway could be helpful for cellular clearance of toxic wastes (55, 56).
  • TFEB transcription factor EB
  • PGC1 ⁇ transcription factor EB
  • TFEB has been shown to rescue the activity of a ⁇ -hexosaminidase mutant.
  • PPAR ⁇ plays a key role in the transcription of Tfeb. Therefore, here, we examined if aspirin could induce the activation of PPAR ⁇ in astrocytes.
  • ESA electrophoretic mobility shift assay
  • Example 15 Aspirin Upregulates TFEB in Primary Mouse Astrocytes Via PPAR ⁇
  • FIG. 15 shows that aspirin induced the expression of TFEB in astrocytes isolated from WT and PPAR ⁇ ( ⁇ / ⁇ ), but not PPAR ⁇ ( ⁇ / ⁇ ), mice.
  • Example 17 Discussion of Examples 10 to 16
  • aspirin has been widely used as an analgesic throughout the world for decades. On the other, it can be taken orally, the least painful route. Although aspirin has been reported to exhibit some toxic effects (gastric ulcers, stomach bleeding, and tinnitus etc.) at high doses (74), in our study, aspirin is boosting lysosomal biogenesis at low doses (2 and 5 ⁇ M) and at low doses, aspirin may not be toxic. However, if aspirin exhibits any toxic effects even at lower doses (e.g. gastric ulcer), there are ways to reduce its side effects.
  • enteric-coated aspirin is available for oral use and to avoid the degradation in the stomach.
  • low dose of aspirin in slow-releasing formulation showed efficacy as an anti-platelet agent (75) without much noticeable side effect.
  • SAM S-adenosyl-methionine

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