U.S. patent application number 11/966851 was filed with the patent office on 2008-08-07 for methods for enhancing exercise performance.
This patent application is currently assigned to the Salk Institute for Biological Studies. Invention is credited to Michael Downes, Ronald M. Evans, Vihang A. Narkar, Yong-Xu Wang, Ruth T. Yu.
Application Number | 20080187928 11/966851 |
Document ID | / |
Family ID | 39589228 |
Filed Date | 2008-08-07 |
United States Patent
Application |
20080187928 |
Kind Code |
A1 |
Evans; Ronald M. ; et
al. |
August 7, 2008 |
METHODS FOR ENHANCING EXERCISE PERFORMANCE
Abstract
Disclosed herein are methods for enhancing one or more effects
of exercise in a subject by administering a PPAR.delta. agonist
(e.g., GW1516) to the subject in combination with an exercise
program. Also disclosed are gene expression profiles unique to the
combination of agonist-induced PPAR.delta. activation and exercise.
Such profiles are useful, at least, in methods for identifying the
use of performance-enhancing drugs in exercised subjects (such as,
professional or athletes). Direct interactions between PPAR.delta.
and exercised-induced kinases (e.g., AMPK or its subunits, AMPK
.alpha.1 and/or AMPK .alpha.2) also are disclosed. Such
protein-protein interactions provide new targets for identification
of useful compounds.
Inventors: |
Evans; Ronald M.; (La Jolla,
CA) ; Narkar; Vihang A.; (San Diego, CA) ;
Wang; Yong-Xu; (Natick, MA) ; Downes; Michael;
(San Diego, CA) ; Yu; Ruth T.; (La Jolla,
CA) |
Correspondence
Address: |
KLARQUIST SPARKMAN, LLP
121 S.W. SALMON STREET, SUITE 1600
PORTLAND
OR
97204
US
|
Assignee: |
the Salk Institute for Biological
Studies
|
Family ID: |
39589228 |
Appl. No.: |
11/966851 |
Filed: |
December 28, 2007 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
60882774 |
Dec 29, 2006 |
|
|
|
Current U.S.
Class: |
435/6.14 ;
514/310; 514/789 |
Current CPC
Class: |
A61K 31/4178 20130101;
A61P 43/00 20180101; A61P 21/00 20180101; A61K 31/426 20130101;
A61K 31/47 20130101; A61P 25/02 20180101; A61P 3/04 20180101; C12Q
2600/158 20130101; C12Q 2600/124 20130101; C12Q 2600/136 20130101;
A61P 21/06 20180101; C12Q 1/6876 20130101 |
Class at
Publication: |
435/6 ; 514/789;
514/310 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68; A61K 31/47 20060101 A61K031/47 |
Goverment Interests
ACKNOWLEDGEMENT OF GOVERNMENT SUPPORT
[0002] This work was supported by National Institutes of Health
Grant No. 1 F32 AR053803-01 (NRSA Fellowship). Therefore, the
Government of the United States has certain rights in this
invention.
Claims
1. A method for enhancing an exercise effect in a subject,
comprising performing by a subject physical activity sufficient to
produce an exercise effect; and administering to the subject an
effective amount of a PPAR.delta. agonist, thereby enhancing the
exercise effect in the subject.
2. The method of claim 1, wherein the subject is a mammal.
3. The method of claim 2, wherein the subject is a racing
mammal.
4. The method of claim 3, wherein the racing mammal is a horse, a
dog, or a human.
5. The method of claim 1, wherein the subject is an adult.
6. The method of claim 1, wherein the subject is an
exercise-trained subject.
7. The method of claim 1, wherein the PPAR.delta. agonist is
GW1516.
8. The method of claim 1, wherein the PPAR.delta. agonist is
administered on the same day(s) on which the physical activity is
performed.
9. The method of claim 1, wherein the physical activity is an
aerobic exercise.
10. The method of claim 9, wherein the aerobic exercise is
running.
11. The method of claim 9, wherein the exercise effect is improved
running endurance.
12. The method of claim 11, wherein improved running endurance is
improved running distance or improved running time or a combination
thereof.
13. The method of claim 1, wherein the effective amount is from
about 5 mg/kg per day to about 10 mg/kg per day in a single dose or
in divided doses.
14. The method of claim 1, wherein administration comprises oral
administration, intravenous injection, intramuscular injection, or
subcutaneous injection.
15. The method of claim 1, wherein the exercise effect is increased
fatty acid oxidation in at least one skeletal muscle of the
subject.
16. The method of claim 1, wherein the exercise effect is body fat
reduction.
17. The method of claim 16, wherein the body fat is white adipose
tissue.
18. A method for identifying the use of performance-enhancing
substances in an exercise-trained subject comprising determining in
a biological sample taken from an exercise-trained subject the
expression of one or more molecules listed in Tables 2 or 4.
19. The method of claim 18, wherein: (i) expression is upregulated
in one or more of adipose differentiation related protein;
stearoyl-Coenzyme A desaturase 2; acetyl-Coenzyme A
acetyltransferase 2; ATP citrate lyase; adiponectin, C1Q and
collagen domain containing; diacylglycerol O-acyltransferase 2;
lipase, hormone sensitive; monoglyceride lipase; resistin; CD36
antigen; fatty acid binding protein 4, adipocyte; lipoprotein
lipase; microsomal glutathione S-transferase 1; GPI-anchored
membrane protein 1; dual specificity phosphatase 7; homeodomain
interacting protein kinase 3; insulin-like growth factor binding
protein 5; protein phosphatase 2 (formerly 2A), regulatory subunit
A (PR 65), beta isoform; protein tyrosine phosphatase-like (proline
instead of catalytic arginine); member b; CCAAT/enhancer binding
protein (C/EBP), alpha; nuclear receptor subfamily 1, group D,
member 2(Reverb-b); transferring; archain 1; solute carrier family
1 (neutral amino acid transporter), member 5; RIKEN cDNA 1810073N04
gene; haptoglobin; retinol binding protein 4, plasma;
phosphoenolpyruvate carboxykinase 1, cytosolic; cell death-inducing
DFFA-like effector c; interferon, alpha-inducible protein 27;
carbonic anhydrase 3; cysteine dioxygenase 1, cytosolic; DNA
segment, Chr 4, Wayne State University 53, expressed; dynein
cytoplasmic 1 intermediate chain 2; Kruppel-like factor 3 (basic);
thyroid hormone responsive SPOT14 homolog (Rattus); cytochrome
P450, family 2, subfamily e, polypeptide 1; complement factor D
(adipsin); and/or transketolase; or (ii) expression is
downregulated in one or more of gamma-glutamyl carboxylase;
3-oxoacid CoA transferase 1; solute carrier family 38, member 4;
annexin A7; CD55 antigen, RIKEN cDNA 1190002H23 gene; fusion,
derived from t(12;16) malignant liposarcoma (human); lysosomal
membrane glycoprotein 2; and/or neighbor of Punc E11; or (iii) a
combination of (i) and (ii).
20. The method of claim 18, wherein determining expression
comprises determining protein expression, determining expression of
a gene encoding the protein, or a combination thereof.
21. The method of claim 20, comprising determining expression of a
gene encoding the protein.
22. The method of claim 18, wherein the biological sample is a
skeletal muscle biopsy.
23. A method of identifying an agent having potential to enhance
exercise performance in a subject, comprising: providing a first
component comprising a PPAR.delta. receptor or an AMPK-binding
fragment thereof; providing a second component comprising an
AMP-activated protein kinase (AMPK), AMPK.alpha.1, AMPK.alpha.2, or
a PPAR.delta.-binding fragment of any thereof; contacting the first
component and the second component with at least one test agent
under conditions that would permit the first component and the
second component to specifically bind to each other in the absence
of the at least one test agent; and determining whether the at
least one test agent affects specific binding of the first
component and the second component to each other, wherein an effect
on specific binding identifies the at least one test agent as an
agent having potential to enhance exercise performance in a
subject.
24. The method of claim 23, further comprising providing a third
component comprising a PPAR.delta. agonist; and contacting the
first component, second component, and third component.
25. The method of claim 24, wherein the PPAR.delta. agonist is
GW1516.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional
Application No. 60/882,774 filed Dec. 29, 2006, herein incorporated
by reference.
FIELD
[0003] This disclosure concerns the use of peroxisome
proliferator-activated receptor (PPAR).delta. agonists for
improving exercise performance in a subject, methods for
identifying substance-enhanced exercise performance in a subject,
and methods for identifying compounds that affect the interaction
of PPAR.delta. with exercise-induced kinases.
BACKGROUND
[0004] Skeletal muscle is an adaptive tissue composed of multiple
myofibers that differ in their metabolic and contractile properties
including oxidative slow-twitch (type I), mixed
oxidative/glycolytic fast-twitch (type IIa) and glycolytic
fast-twitch (type IIb) myofibers (Fluck et al., Rev. Physiol.
Biochem. Pharmacol., 146:159-216, 2003; Pette and Staron, Microsc.
Res. Tech., 50:500-509, 2000). Type I muscle fibers preferentially
express enzymes that oxidize fatty acids, contain slow isoforms of
contractile proteins and are more resistant to fatigue than are
glycolytic muscle fibers (Fluck et al., Rev. Physiol. Biochem.
Pharmacol., 146:159-216, 2003; Pette and Staron, Microsc. Res.
Tech., 50:500-509, 2000). Type II fibers preferentially metabolize
glucose and express the fast isoforms of contractile proteins
(Fluck et al., Rev. Physiol. Biochem. Pharmacol., 146:159-216,
2003; Pette and Staron, Microsc. Res. Tech., 50:500-509, 2000).
[0005] Endurance exercise training triggers a complex remodeling
program in skeletal muscle that progressively enhances performance
in athletes such as marathon runners, mountain climbers and
cyclists. This involves changes in metabolic programs and
structural proteins within the myofibers that alter the energy
substrate utilization and contractile properties that act to reduce
muscle fatigue (Fluck et al., Rev. Physiol. Biochem. Pharmacol.,
146:159-216, 2003; Pette and Staron, Microsc. Res. Tech.,
50:500-509, 2000). Training based adaptations in the muscle are
linked to increases in the expression of genes involved in the
slow-twitch contractile apparatus, mitochondrial respiration and
fatty acid oxidation (Holloszy and Coyle, J. Appl. Physiol.,
56:831-838, 1984; Booth and Thomason, Physiol. Rev., 71:541-585,
1991; Schmitt et al., Physiol. Genomics, 15:148-157, 2003; Yoshioka
et al., FASEB J, 17:1812-1819, 2003; Mahoney et al., FASEB J,
19:1498-1500, 2005; Mahoney and Tarnopolsky, Phys. Med. Rehabil.
Clin. N. Am., 16:859-873, 2005; Siu et al., J. Appl. Physiol.,
97:277-285, 2004; Garnier et al., FASEB J, 19:43-52, 2005; Short et
al., J. Appl. Physiol., 99:95-102, 2005; Timmons et al., FASEB J,
19:750-760, 2005). Such exercise training-related adaptations can
improve performance and protect against obesity and related
metabolic disorders (Wang et al., PLoS Biol., 2:e294, 2004; Koves
et al., J. Biol. Chem., 280:33588-33598, 2005). Moreover, skeletal
muscles rich in oxidative slow-twitch fibers are resistant to
muscle wasting (Minnaard et al., Muscle Nerve. 31: 339-48,
2005).
[0006] PPARs are members of the nuclear receptor superfamily of
ligand-inducible transcription factors. They form heterodimers with
retinoid X receptors (RXRs) and bind to consensus DNA sites
composed of direct repeats of hexameric DNA sequences separated by
1 bp. In the absence of ligand, PPAR-RXR heterodimers recruit
corepressors and associated histone deacetylases and
chromatin-modifying enzymes, silencing transcription by so-called
active repression (Ordentlich et al., Curr. Top. Microbiol.
Immunol., 254:101-116, 2001; Jepsen and Rosenfeld, J. Cell Sci.,
115:689-698, 2002; Privalsky, Ann. Rev. Physiol., 66:315-360,
2004). Ligand binding induces a conformational change in PPAR-RXR
complexes, releasing repressors in exchange for coactivators.
Ligand-activated complexes recruit the basal transcriptional
machinery, resulting in enhanced gene expression. PPARs bind to
lower-affinity ligands generated from dietary fat or intracellular
metabolism. In keeping with their roles as lipid sensors,
ligand-activated PPARs turn on feed-forward metabolic cascades to
regulate lipid homeostasis via the transcription of genes involved
in lipid metabolism, storage, and transport.
[0007] Three PPAR isotypes exist in mammals: .alpha. (also known as
NR1C1), .gamma. (also known as NR1C3), and .beta. (also known as
.beta. or NR1C2). PPAR.delta. is expressed in most cell types with
relative abundance (Smith, Biochem. Soc. Trans., 30(6):1086-1090,
2002), which led to early speculation that it may serve a "general
housekeeping role" (Kliewer et al., Proc. Natl. Acad. Sci. U.S.A.,
91:7355-7359, 1994). More recently, PPAR.delta. transgenic mouse
models and discoveries aided by the development of high-affinity
PPAR.delta. agonists have revealed PPAR.delta. as a key
transcriptional regulator with effects in diverse tissues including
fat, skeletal muscle, and the heart (for review see, e.g., Barish
et al., J. Clin. Invest., 116(3):590-597, 2006).
[0008] Targeted expression of a constitutively active PPAR.delta.
receptor (VP16-PPAR.delta.) transgene in rodent skeletal muscle
promoted remodeling of skeletal muscle to an oxidative phenotype
and increased running endurance in unexercised adult mice (Wang et
al., PLoS Biol., 2:e294, 2004). The observed PPAR.delta.-mediated
reprogramming of muscle fibers involved the increased expression of
genes related to fatty acid oxidation, mitochondrial respiration,
oxidative metabolism, and slow-twitch contractile apparatus (Wang
et al., PLoS Biol., 2:e294, 2004). These VP16-PPAR.delta.
transgenic mice, who had a phenotype similar to endurance-trained
athletes, but who had had no exercise training, suggest that
pharmacological activation of endogenous PPAR.delta. in an adult,
sedentary subject might provide an exercise effect without the
actual exercise. Given the numerous benefits of exercise on general
health, identification of orally active agents that mimic the
effects of exercise is a long standing, albeit elusive medical
goal.
SUMMARY
[0009] This disclosure illustrates that, despite expectations to
the contrary, pharmacological activation of endogenous PPAR.delta.
in adult, sedentary subjects did not promote remodeling of skeletal
muscle to an oxidative phenotype or increase running endurance in
such subjects. Surprisingly, however, pharmacological activation of
PPAR.delta. in combination with at least sub-maximal exercise
synergistically modified skeletal muscle architecture (e.g.,
induced fatigue resistant type I fiber specification and
mitochondrial biogenesis) and increased exercise performance (e.g.,
running endurance). In addition, agonist-induced activation of
endogenous PPAR.delta. in combination with exercise led to a unique
"gene expression signature" in skeletal muscle, which was distinct
from the gene expression profile obtained by either exercise or
drug intake alone, and revealed direct interactions between
PPAR.delta. and exercise-induced kinases (such as AMPK .alpha.1
and/or AMPK .alpha.2).
[0010] These and other discoveries described herein serve as the
basis for disclosed methods. For example, it can now be appreciated
that PPAR.delta. agonists (e.g., GW1516) used in combination with
exercise can enhance exercise-induced effects, such as to improve
exercise endurance (e.g., running endurance) even more than may be
achieved by exercise alone. In another example, the expression of
one or more genes and/or proteins that are uniquely regulated by
the combination of exercise and PPAR.delta. agonist administration
can be used to identify subjects using drugs to enhance exercise
performance. In still other examples, the newly identified protein
complexes, including PPAR.delta. and exercise-induced kinases (such
as AMPK .alpha.1 and/or AMPK .alpha.2), can be used to identify
agents that have potential to affect PPAR.delta.-regulated gene
networks and the corresponding downstream biochemical and/or
physiological effects.
[0011] The foregoing and other features will become more apparent
from the following detailed description of several embodiments,
which proceeds with reference to the accompanying figures.
BRIEF DESCRIPTION OF THE FIGURES
[0012] FIG. 1A is a series of bar graphs showing the effects of
orally administered PPAR.delta. agonist (GW1516) on mRNA expression
levels of three biomarkers of fatty acid oxidation, uncoupling
protein 3 (UCP3), carnitine palmitoyl-transferase I (mCPT I), and
pyruvate dehydrogenase kinase, isoenzyme 4 (PDK4), in quadriceps
muscle isolated from sedentary vehicle-treated (V), sedentary
GW1516-treated (GW), sedentary VP16-PPAR.delta. transgenic (TG),
and sedentary wild-type littermates of VP16-PPAR.delta. transgenic
mice (WT). Data are presented as mean .+-.SEM of N=4-9 mice each
analyzed in triplicate. * Represents a statistically significant
difference between V and GW1516 groups (p<0.05, unpaired
student's t-test), or TG and WT groups (p<0.05, unpaired
student's t-test).
[0013] FIG. 1B-D are a series of bar graphs showing the regulation
of oxidative genes UCP3, mCPT I, and PDK4 by GW1516 (GW) in
wild-type (WT) and PPAR.delta. null (KO) primary muscle cells. *
represents statistical significance between V and indicated groups
(p<0.05, One Way ANOVA; post hoc: Dunnett's Multiple Comparison
Test)
[0014] FIG. 1E is a series of bar graphs showing running endurance
of vehicle-treated sedentary (V; open bars) and GW1516-treated
sedentary (GW; black bars) mice before (Week 0) and after (Week 5)
treatment. Running endurance is quantified by the amount of time
for which (left panel) or the distance (right panel) animals in
each group ran on the treadmill. Data is represented as mean .+-.SD
values from N=6 mice.
[0015] FIGS. 2A-C show the effects of administration of a
PPAR.delta. agonist, GW1516, on the gastrocnemius muscle of
sedentary (V or GW) or trained (Tr or Tr+GW) mice. FIG. 2A shows
digital images of representative meta-chromatically stained frozen
cross-sections of gastrocnemius muscle from vehicle-treated,
sedentary (V), GW1516-treated, sedentary (GW), vehicle-treated,
exercised (Tr) and GW1516-treated, exercised (Tr+GW) mice. Type I
(slow oxidative) fibers are darkly stained. FIG. 2B is a bar graph
showing the percentage of type I fibers (as a percentage of the
total fibers) in V, GW, Tr, and Tr+GW gastrocnemius (N=3).
[0016] FIG. 2C is a bar graph showing the fold change in
mitochondrial DNA to nuclear DNA ratio in V (left bar), GW (left
center bar), Tr (right center bar), and Tr+GW (right bar) groups of
mice (N=9). Data in (B) and (C) are presented as mean .+-.SEM. In
each bar graph, * represents a statistical difference between V and
the group(s) indicated by asterisk (p<0.05, One-Way ANOVA; post
hoc: Dunnett's Multiple Comparison Test).
[0017] FIGS. 3A-C are a series of bar graphs showing gene
expression in quadriceps muscle isolated from V, GW, Tr and Tr+GW
groups. FIG. 3A shows the relative gene expression levels of
biomarkers for fatty acid oxidation (UCP3, mCPT I, PDK4; from left
to right). FIG. 3B shows the relative gene expression levels of
biomarkers for fatty acid storage (SCD1, FAS, SREBP1c). FIG. 3C
shows the relative gene expression levels of biomarkers for fatty
acid uptake (FAT/CD36, LPL). Data is presented as mean .+-.SEM of
N=9 mice, each analyzed in triplicate. * represents statistically
significant difference between V and the group(s) indicated by
asterisk (p<0.05, One Way ANOVA; post hoc: Dunnett's Multiple
Comparison Test).
[0018] FIG. 3D shows images of Western blots illustrating protein
expression levels of oxidative biomarkers (myoglobin, UCP3, CYCS,
SCD1) and loading control (tubulin) in protein lysates prepared
from quadriceps (N=3).
[0019] FIG. 4 shows a graph of muscle triglyceride levels in
gastrocnemius muscle of V, GW, Tr and Tr+GW mice. Data is presented
as mean .+-.SEM of N=9 mice, each analyzed in triplicate. *
represents statistical significance between V and group(s)
indicated by asterisk (*p<0.05, One Way ANOVA; post
hoc:Dunnett's Multiple Comparison Test).
[0020] FIGS. 5A and B are bar graphs showing the effects of GW1516
treatment on running endurance in exercise-trained mice. Bar graphs
of the (A) time and (B) distance that vehicle-(V; open bars) and
GW1516-treated (GW; black bars) mice ran on a treadmill before
(Week 0) and after (Week 5) exercise training. Data is represented
as mean .+-.SD of N=6 mice. *** represents statistically
significant difference between V and GW groups (p<0.001; One Way
ANOVA; post hoc:Tukey's Multiple Comparison Test).
[0021] FIG. 5C is a bar graph showing epididymal white adipose to
body weight ratio in V, GW, Tr and Tr+GW mice. Data is presented as
mean .+-.SEM of N=9 mice, each analyzed in triplicate. * represents
statistical significance between V and group(s) indicated by
asterisk (*p<0.05, One Way ANOVA; post hoc:Dunnett's Multiple
Comparison Test).
[0022] FIG. 5D shows digital images of H&E-stained
cross-sections of epididymal white adipose from V, GW, Tr and Tr+GW
mice. Similar results were obtained from N=3 mice. * represents
statistical significance between V and group(s) indicated by
asterisk (*p<0.05, One Way ANOVA; post hoc:Dunnett's Multiple
Comparison Test).
[0023] FIG. 6 shows a Venn diagram comparing GW, Tr and Tr+GW
target genes identified in microarray analysis of quadriceps. Data
is an average of N=3 samples in each group. The selection criteria
used a p<0.05 on Bonferroni's multiple comparison test and a
fold change greater than 1.5.
[0024] FIG. 7A is a series of Western blot images showing AMPK
activation by exercise. The levels of phospho-AMPK (phospho-AMPK)
and total-AMPK in quadriceps muscle of sedentary (Sed/C57B1) and
exercise-trained (Tr/C57B1) mice (N=5-7) are shown.
[0025] FIG. 7B is a series of Western blot images showing AMPK
activation by VP16-PPARd over-expression. The levels of
phospho-AMPK (phospho-AMPK) and total-AMPK in quadriceps muscle of
sedentary wild-type or transgenic mice (Sed/WT or Sed/TG) are
shown.
[0026] FIGS. 8A-B show the synergistic regulation of muscle gene
expression by PPAR.delta. and AMPK. (A) Venn diagram comparing GW,
AI, and AI+GW target genes identified in microarray analysis of
quadriceps. Data is an average of N=3 samples in each group. The
selection criteria used a p<0.05 on Bonferroni's multiple
comparison test and fold change greater than 1.5. (B) Comparison of
Tr+GW and AI+GW dependent gene signatures identified in quadriceps.
Data is an average of N=3 samples in each group. The selection
criteria used is similar to one used in FIG. 8A.
[0027] FIGS. 9A-H show the expression of (A) UCP3, (B) mCPT I, (C)
PDK4, (D) SCD1, (E) ATP citrate lyase, (F) HSL, (G) mFABP, and (H)
LPL transcripts in quadriceps of mice treated with vehicle (V),
GW1516 (GW), AICAR (AI) and the combination of the two drugs
(GW+AI) for 6 days. Data is presented as mean .+-.SEM of N=6 mice
in each group, analyzed in triplicate. * Indicates statistically
significant difference between V and indicated groups (p<0.05,
One Way ANOVA; post hoc: Dunnett's Multiple Comparison Test).
[0028] FIGS. 10A-L demonstrate the AMPK-PPAR.delta. interaction.
(A-D) show the expression of metabolic genes in wild type and
PPAR.delta. null (KO) primary muscle cells treated with V, GW, AI
and GW+AI (bars from left to right) for 24 hours. In (E-F, J),
AD293 cells were transfected with PPAR.delta.+RXR.alpha.+Tk-PPRE
along with control vector, AMPK .alpha.1, .alpha.2 and/or
PGC1.alpha. as indicated above. (E) Induction of basal PPAR.delta.
transcriptional activity by AMPK .alpha.1 or .alpha.2. (F)
Dose-dependent induction of PPAR.delta. transcriptional activity is
enhanced by AMPK .alpha.1 (closed circle) or AMPK .alpha.2 (closed
square) compared to control (open triangle). In (G-I, K), AD293
cells were transfected and processed as indicated. (G-H)
Representative blot showing co-immunoprecipitation of transfected
(G) or endogenous (H) AMPK with Flag-PPAR.delta.. (I) Metabolic p32
labeling of PPAR.delta. in AD293 cells transfected as described.
(J) Synergistic regulation of basal (V) and ligand (GW) dependent
PPAR.delta. transcriptional activity by AMPK .alpha.2 subunit and
PGC1.alpha. (K) Co-immunoprecipitation of PPAR.delta. but not AMPK
.alpha.2 subunit with Flag-PGC1.alpha. (L) Model depicting
exercise-PPAR.delta. interaction in re-programming muscle
genome.
SEQUENCE INFORMATION
[0029] Nucleic acid and amino acid sequences may be referred to
herein by GenBank accession number. It is understood that the
sequences given such GenBank accession numbers are incorporated by
reference as they existed and were known as of Dec. 29, 2006.
DETAILED DESCRIPTION
I. Introduction
[0030] Disclosed herein are methods for enhancing an exercise
effect in a subject including the steps of performing by a subject
physical activity (such as aerobic exercise (e.g., running))
sufficient to produce an exercise effect; and administering to the
subject an effective amount of a PPAR.delta. agonist (e.g.,
GW1516). The exercise effect that is enhanced can be, for example,
improved running endurance (such as, improved running distance or
improved running time or a combination thereof, increased fatty
acid oxidation in at least one skeletal muscle of the subject,
and/or body fat (e.g., white adipose tissue) reduction). In some
method embodiments, a subject is a mammal (such as a racing mammal,
like a horse, a dog, or a human), and/or an adult, and/or an
exercise-trained subject. In other exemplary methods, the
PPAR.delta. agonist is administered on the same day(s) on which the
physical activity is performed. In some methods, administration of
the PPAR.delta. agonist is by oral administration, intravenous
injection, intramuscular injection, and/or subcutaneous injection.
In other method embodiments, the effective amount of the
PPAR.delta. agonist is from about 1 mg per day to about 20 mg per
day in a single dose or in divided doses.
[0031] Also disclosed herein are methods for identifying the use of
performance-enhancing substances in an exercise-trained subject,
which include determining in a biological sample taken from an
exercise-trained subject (e.g. a skeletal muscle biopsy) the
expression of the molecules listed in Table 2 or listed in Table 4,
or a subset thereof, such as expression of at least 1, at least 5,
at least 10, at least 20, at least 40 of the molecules listed in
Table 2 or in Table 4.
[0032] In some methods for identifying the use of
performance-enhancing substances in an exercise-trained subject,
(i) expression is upregulated in one or more of (such as at least
5, at least 10, at least 20, at least 35, or all of) adipose
differentiation related protein; stearoyl-Coenzyme A desaturase 2;
acetyl-Coenzyme A acetyltransferase 2; ATP citrate lyase;
adiponectin, C1Q and collagen domain containing; diacylglycerol
O-acyltransferase 2; lipase, hormone sensitive; monoglyceride
lipase; resistin; CD36 antigen; fatty acid binding protein 4,
adipocyte; lipoprotein lipase; microsomal glutathione S-transferase
1; GPI-anchored membrane protein 1; dual specificity phosphatase 7;
homeodomain interacting protein kinase 3; insulin-like growth
factor binding protein 5; protein phosphatase 2 (formerly 2A),
regulatory subunit A (PR 65), beta isoform; protein tyrosine
phosphatase-like (proline instead of catalytic arginine); member b;
CCAAT/enhancer binding protein (C/EBP), alpha; nuclear receptor
subfamily 1, group D, member 2(Reverb-b); transferring; archain 1;
solute carrier family 1 (neutral amino acid transporter), member 5;
RIKEN cDNA 1810073N04 gene; haptoglobin; retinol binding protein 4,
plasma; phosphoenolpyruvate carboxykinase 1, cytosolic; cell
death-inducing DFFA-like effector c; interferon, alpha-inducible
protein 27; carbonic anhydrase 3; cysteine dioxygenase 1,
cytosolic; DNA segment, Chr 4, Wayne State University 53,
expressed; dynein cytoplasmic 1 intermediate chain 2; Kruppel-like
factor 3 (basic); thyroid hormone responsive SPOT14 homolog
(Rattus); cytochrome P450, family 2, subfamily e, polypeptide 1;
complement factor D (adipsin); and/or transketolase; and/or (ii)
expression is downregulated in one or more of gamma-glutamyl
carboxylase; 3-oxoacid CoA transferase 1; solute carrier family 38,
member 4; annexin A7; CD55 antigen; RIKEN cDNA 1190002H23 gene;
fusion, derived from t(12;16) malignant liposarcoma (human);
lysosomal membrane glycoprotein 2; and/or neighbor of Punc E11,
such as 1, 2, 3, 4, 5, 6, 7, 8 or 9 of these molecules.
[0033] Exemplary methods for identifying the use of
performance-enhancing substances in an exercise-trained subject
involve determining protein expression and/or determining
expression of a gene encoding the protein. Such methods are routine
in the art. In some examples, the level of protein or nucleic acid
expression is quantified.
[0034] Methods of identifying an agent having potential to enhance
exercise performance in a subject also are disclosed herein. Such
methods can include (i) providing a first component comprising a
PPAR.delta. receptor or an AMPK-binding fragment thereof; (ii)
providing a second component comprising an AMP-activated protein
kinase (AMPK), AMPK.alpha.1, AMPK.alpha.2, or a PPAR.delta.-binding
fragment of any thereof; (iii) contacting the first component and
the second component with at least one test agent under conditions
that would permit the first component and the second component to
specifically bind to each other in the absence of the at least one
test agent; and (iv) determining whether the at least one test
agent affects the specific binding of the first component and the
second component to each other. An effect on specific binding of
the first component and the second component to each other
identifies the at least one test agent as an agent having potential
to enhance exercise performance in a subject.
[0035] In some methods of identifying an agent having potential to
enhance exercise performance a third component, i.e., a PPAR.delta.
agonist (e.g., GW1516), is involved and the first component, second
component, and third component are contacted as described
above.
II. Abbreviations and Terms
[0036] AMPK AMP-activated protein kinase
[0037] bps Beats per second
[0038] MAPK Mitogen-activated protein kinase
[0039] mCPT I Muscle carnitine palmitoyl transferase I
[0040] QPCR or qPCR Quantitative PCR
[0041] PDK4 Pyruvate dehydrogenase kinase 4
[0042] PES Performance-enhancing substance(s)
[0043] PPAR Peroxisome proliferator-activated receptors
[0044] UCP3 Uncoupling protein 3
[0045] Unless otherwise explained, all technical and scientific
terms used herein have the same meaning as commonly understood by
one of ordinary skill in the art to which the disclosed subject
matter belongs. Definitions of common terms in molecular biology
may be found in Benjamin Lewin, Genes V, published by Oxford
University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.),
The Encyclopedia of Molecular Biology, published by Blackwell
Science Ltd., 1994 (ISBN 0-632-02182-9); and/or Robert A. Meyers
(ed.), Molecular Biology and Biotechnology: A Comprehensive Desk
Reference, published by VCH Publishers, Inc., 1995 (ISBN
1-56081-569-8). In order to facilitate review of various
embodiments of the disclosure, the following explanations of
specific terms are provided:
[0046] Expression: The process by which the coded information of a
nucleic acid transcriptional unit (including, for example, genomic
DNA or cDNA) is converted into an operational, non-operational, or
structural part of a cell, often including the synthesis of a
polypeptide. Gene expression can be influenced by external signals;
for instance, exposure of a cell, tissue or subject to an agent
that enhances gene expression. Expression of a gene also may be
regulated anywhere in the pathway from DNA to RNA to polypeptide.
Regulation of gene expression occurs, for instance, through
controls acting on transcription, translation, RNA transport and
processing, degradation of intermediary molecules such as mRNA, or
through activation, inactivation, compartmentalization or
degradation of specific protein molecules after they have been
made, or by combinations thereof. Gene expression (for example
expression of one or more of the genes listed in Tables 2 and 4)
can be measured at the RNA level or the protein level and by any
method known in the art, including, without limitation, Northern
blot, RT-PCR, Western blot, or in vitro, in situ, or in vivo
protein activity assay(s).
[0047] The expression of a nucleic acid may be modulated compared
to a control state, such as at a control time (for example, prior
to administration of a substance or agent that affects regulation
of the nucleic acid under observation) or in a control cell or
subject, or as compared to another nucleic acid. Such modulation
includes but is not necessarily limited to overexpression,
underexpression, or suppression of expression. In addition, it is
understood that modulation of nucleic acid expression may be
associated with, and in fact may result in, a modulation in the
expression of an encoded polypeptide or even a polypeptide that is
not encoded by that nucleic acid (such as downstream regulated
polypeptide(s)).
[0048] The expression of a polypeptide also may be modulated
compared to a control state, such as at a control time (for
example, prior to administration of a substance or agent that
affects expression of a nucleic acid encoding or regulating the
polypeptide) or in a control cell or subject, or as compared to
another polypeptide. Modulation of polypeptide expression includes,
but is not limited to, overexpression or decreased expression of
the polypeptide, alteration of the subcellular localization or
targeting of the polypeptide, alteration of the temporally
regulated expression of the polypeptide (such that the polypeptide
is expressed when it normally would not be, or alternatively is not
expressed when it normally would be), alteration in the stability
of the polypeptide, alteration in the spatial localization of the
protein (such that the polypeptide is not expressed where it would
normally be expressed or is expressed where it normally would not
be expressed).
[0049] Isolated: An "isolated" biological component (such as a
polynucleotide, polypeptide, or cell) has been purified away from
other biological components in a mixed sample (such as a cell or
tissue extract). For example, an "isolated" polypeptide or
polynucleotide is a polypeptide or polynucleotide that has been
separated from the other components of a cell in which the
polypeptide or polynucleotide was present (such as an expression
host cell for a recombinant polypeptide or polynucleotide).
[0050] The term "purified" refers to the removal of one or more
extraneous components from a sample. For example, where recombinant
polypeptides are expressed in host cells, the polypeptides are
purified by, for example, the removal of host cell proteins thereby
increasing the percent of recombinant polypeptides in the sample.
Similarly, where a recombinant polynucleotide is present in host
cells, the polynucleotide is purified by, for example, the removal
of host cell polynucleotides thereby increasing the percent of
recombinant polynucleotide in the sample. Isolated polypeptides or
nucleic acid molecules, typically, comprise at least 50%, at least
60%, at least 70%, at least 80%, at least 90%, at least 95% or even
over 99% (w/w or w/v) of a sample.
[0051] Polypeptides and nucleic acid molecules are isolated by
methods commonly known in the art and as described herein. Purity
of polypeptides or nucleic acid molecules may be determined by a
number of well-known methods, such as polyacrylamide gel
electrophoresis for polypeptides, or agarose gel electrophoresis
for nucleic acid molecules.
[0052] Sequence identity: The similarity between two nucleic acid
sequences or between two amino acid sequences is expressed in terms
of the level of sequence identity shared between the sequences.
Sequence identity is typically expressed in terms of percentage
identity; the higher the percentage, the more similar the two
sequences.
[0053] Methods for aligning sequences for comparison are well known
in the art. Various programs and alignment algorithms are described
in: Smith and Waterman, Adv. Appl. Math. 2:482, 1981; Needleman and
Wunsch, J. Mol. Biol. 48:443, 1970; Pearson and Lipman, Proc. Natl.
Acad. Sci. USA 85:2444, 1988; Higgins and Sharp, Gene 73:237-244,
1988; Higgins and Sharp, CABIOS 5:151-153, 1989; Corpet et al.,
Nucleic Acids Research 16:10881-10890, 1988; Huang, et al.,
Computer Applications in the Biosciences 8:155-165, 1992; Pearson
et al., Methods in Molecular Biology 24:307-331, 1994; Tatiana et
al., (1999), FEMS Microbiol. Lett., 174:247-250, 1999. Altschul et
al. present a detailed consideration of sequence alignment methods
and homology calculations (J. Mol. Biol. 215:403-410, 1990).
[0054] The National Center for Biotechnology Information (NCBI)
Basic Local Alignment Search Tool (BLAST.TM., Altschul et al., J.
Mol. Biol. 215:403-410, 1990) is available from several sources,
including the National Center for Biotechnology Information (NCBI,
Bethesda, Md.) and on the Internet, for use in connection with the
sequence-analysis programs blastp, blastn, blastx, tblastn and
tblastx. A description of how to determine sequence identity using
this program is available on the internet under the help section
for BLAST.TM..
[0055] For comparisons of amino acid sequences of greater than
about 30 amino acids, the "Blast 2 sequences" function of the
BLAST.TM. (Blastp) program is employed using the default BLOSUM62
matrix set to default parameters (cost to open a gap [default=5];
cost to extend a gap [default=2]; penalty for a mismatch
[default=-3]; reward for a match [default=1]; expectation value (E)
[default=10.0]; word size [default=3]; number of one-line
descriptions (V) [default=100]; number of alignments to show (B)
[default=100]). When aligning short peptides (fewer than around 30
amino acids), the alignment should be performed using the Blast 2
sequences function, employing the PAM30 matrix set to default
parameters (open gap 9, extension gap 1 penalties). Proteins with
even greater similarity to the reference sequences will show
increasing percentage identities when assessed by this method.
[0056] For comparisons of nucleic acid sequences, the "Blast 2
sequences" function of the BLAST.TM. (Blastn) program is employed
using the default BLOSUM62 matrix set to default parameters (cost
to open a gap [default=11]; cost to extend a gap [default=1];
expectation value (E) [default=10.0]; word size [default=11];
number of one-line descriptions (V) [default=100]; number of
alignments to show (B) [default=100]). Nucleic acid sequences with
even greater similarity to the reference sequences will show
increasing percentage identities when assessed by this method.
[0057] Specific binding: Specific binding refers to the particular
interaction between one binding partner (such as a binding agent)
and another binding partner (such as a target). Such interaction is
mediated by one or, typically, more noncovalent bonds between the
binding partners (or, often, between a specific region or portion
of each binding partner). In contrast to non-specific binding
sites, specific binding sites are saturable. Accordingly, one
exemplary way to characterize specific binding is by a specific
binding curve. A specific binding curve shows, for example, the
amount of one binding partner (the first binding partner) bound to
a fixed amount of the other binding partner as a function of the
first binding partner concentration. As the first binding partner
concentration increases under these conditions, the amount of the
first binding partner bound will saturate. In another contrast to
non-specific binding sites, specific binding partners involved in a
direct association with each other (e.g., a protein-protein
interaction) can be competitively removed (or displaced) from such
association (e.g., protein complex) by excess amounts of either
specific binding partner. Such competition assays (or displacement
assays) are very well known in the art.
[0058] The singular terms "a," "an," and "the" include plural
referents unless context clearly indicates otherwise. Similarly,
the word "or" is intended to include "and" unless the context
clearly indicates otherwise. "Comprising" means "including." Hence
"comprising A or B" means "including A or B", or "including A and
B."
[0059] Materials, methods, and examples are illustrative only and
not intended to be limiting. Methods and materials similar or
equivalent to those described herein can be used in the practice or
testing of the present disclosure (see, e.g., Sambrook et al.,
Molecular Cloning: A Laboratory Manual, 2d ed., Cold Spring Harbor
Laboratory Press, 1989; Sambrook et al., Molecular Cloning: A
Laboratory Manual, 3d ed., Cold Spring Harbor Press, 2001; Ausubel
et al., Current Protocols in Molecular Biology, Greene Publishing
Associates, 1992 (and Supplements to 2000); Ausubel et al., Short
Protocols in Molecular Biology: A Compendium of Methods from
Current Protocols in Molecular Biology, 4th ed., Wiley & Sons,
1999; Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring
Harbor Laboratory Press, 1990; and Harlow and Lane, Using
Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory
Press, 1999).
III. Methods of Enhancing an Exercise Effect
[0060] Exercise is known to have many effects on subjects that
perform it. Exercise effects at the molecular, biochemical, and/or
cellular levels (e.g., modified regulation of genes and/or gene
networks and corresponding proteins involved in energy substrate
utilization and contractile properties of muscle) form the basis of
physiological effects that are observed at the tissue, organ,
and/or whole body levels (e.g., increased cardiorespiratory
endurance, muscular strength, muscular endurance, and/or
flexibility, and/or improvements in body appearance). Disclosed
herein are methods for enhancing one or more exercise effects by
combining, at least, physical activity with administration of one
or more PPAR.delta. agonists. In some examples, physical activity
is replaced with administration of an AMPK activator (e.g.,
AICAR).
[0061] In general terms, exercise is the performance of some
physical activity. A single episode (also referred to as a bout) of
physical activity is performed for a particular duration and at a
particular intensity. If more than one bout of exercise is
performed, separate bouts of exercise may have the same or
different durations and/or the same or different intensities.
[0062] In some method embodiments, a single bout of exercise may
last for up to 30 minutes, up to 45 minutes, up to 60 minutes, up
to 90 minutes, up to 2 hours, up to 2.5 hours, up to 3 hours, or
even longer. Typically, in the absence of a prior exercise history,
repeated episodes of physical activity are needed to achieve an
exercise-induced effect (such as, increased aerobic capacity or
increase running endurance). Thus, in some disclosed methods, bouts
of physical activity may be repeated within a single day; for
instance, up to 2 bouts of exercise per day, up to 3 bouts of
exercise per day, up to 4 bouts of exercise per day, up to 5 bouts
of exercise per day, or even more bouts per day. Some professional
athletes or racing mammals may exercise in repeated bouts for a
total of 8 hours or more a day. In other method embodiments, bouts
(or repeated bouts) of exercise are performed on a daily basis, 6
times per week, 5 times per week, 4 times per week or 3 times per
week. In at least some of the disclosed methods, exercise may
continue for at least 2 weeks, for at least 4 weeks, for at least 6
weeks, for at least 3 months, for at least 6 months, for at least 1
year, for at least 3 years, or indefinitely (for the lifetime of
the subject).
[0063] Exercise generally is performed at an intensity that is more
than the usual (e.g., average, median, normal standard, or
normoactive) activity for a subject, and/or at or less than the
maximum activity achievable by a subject performing a particular
exercise. Any known indicator of physical performance can be used
to determine whether a subject is performing more than a usual
amount of activity, including, for instance, measuring heart rate,
repetition rate (e.g., revolutions per second, minutes per mile,
lifts per minute, and many others), and/or force output. In some
methods, a bout of exercise is performed at sub-maximal intensity;
for instance, at about 10% maximal intensity, 25% maximal
intensity, 50% maximal intensity, or 75% maximal intensity. In
other methods, a bout of exercise is performed at 40%-50% maximal
heart rate, 50%-60% maximal heart rate, 60%-70% maximal heart rate,
or 75%-80% maximal heart rate, where maximum heart rate for a human
subject is calculated as: 220 bps-(age of the subject).
[0064] Exercise is generally grouped into three types: (i)
flexibility exercise (such as, stretching), which is believed to,
at least, improve the range of motion of muscles and joints; (ii)
aerobic exercise; and (iii) anaerobic exercise (such as, weight
training, functional training or sprinting) which is believed to,
at least, increase muscle strength and mass.
[0065] Aerobic exercise refers to a physical activity in which
oxidative or aerobic metabolism (as compared to glycolytic or
anaerobic metabolism) substantially predominates in exercised
skeletal muscles. In particular method embodiments, a subject
performs one or more aerobic exercises. Exemplary aerobic exercises
include, without limitation, aerobics, calisthenics, cycling,
dancing, exercise machines (rowing machine, cycling machine (e.g.,
inclined or upright), climbing machine, elliptical trainers, and/or
skiing machines), basketball, football, baseball, soccer, footbag,
housework, jogging, martial arts, massage, pilates, rowing,
running, skipping, swimming, walking, yoga, boxing, gymnastics,
badminton, cricket, track and field, golf, ice hockey, lacrosse,
rugby, tennis, or combinations thereof.
[0066] The disclosed methods contemplate enhancing any known or
observable effect of exercise (such as an aerobic exercise, like
walking or running). In particular methods, running endurance
(e.g., running distance and/or running time) is enhanced.
[0067] Enhancing an exercise effect (such as running endurance)
means that such effect is improved in a subject more than would
have occurred by exercise alone. In some method embodiments, an
enhanced exercise effect is determined by discontinuing
administration of a PPAR.delta. agonist in the subject and
observing (e.g., qualitatively or quantitatively) a reduction in
the exercise effect of interest (e.g., aerobic endurance, such as
running endurance). In some instances, an exercise effect of
interest, the PPAR.delta.-enhanced portion of which is lost upon
discontinuance of PPAR.delta. administration, will be reduced by at
least about 5%, by at least about 10%, by at least about 20%, by at
least about 30%, or by at least about 50% as compared to the
magnitude of the effect with exercise alone.
[0068] A. PPAR.delta. Agonists
[0069] The disclosed methods envision the use of any PPAR.delta.
agonist. Preferably such agonist would be non-toxic in the subject
to which it is administered. Exemplary PPAR.delta. agonists include
GW1516, L-165041 (as described by, e.g., Leibowitz et al., FEBS
Lett., 473(3):333-336, 2000), any one or more compounds described
in PCT Publication Nos. WO/2006/018174, WO/2005/113506,
WO/2005/105754, WO/2006/041197, WO/2006/032023, WO/01/00603,
WO/02/092590, WO/97/28115, WO/97/28149, WO/97/27857, WO/97/28137,
WO/97/27847, and/or WO/98/27974, and/or a published U.S. national
phase application or issued U.S. patent corresponding to any of the
foregoing (each of which is expressly incorporated herein by
reference). Moreover, other PPAR.delta. agonists can be identified
using the methods described, for example, in PCT Publication No.
WO/1998/049555 or any corresponding published U.S. national phase
application or issued U.S. patent (each of which is expressly
incorporated herein by reference).
[0070] In a specific example, the PPAR.delta. agonist is GW1516
(also referred to in the art as GW501516). GW1516 is
(2-methyl-4(((4-methyl-2-(4-trifluoromethylphenyl)-1,3-thiazol-5-yl)methy-
l)sulfanyl)phenoxy)acetic acid as has been shown to be is bioactive
in humans (Sprecher et al., Arterioscler. Thromb. Vasc. Biol.
27(2): 359-65, 2007). In specific examples, GW1516 is administered
orally, for example 1 mg-20 mg/day, such as 2.5 mg or 10 mg per
day.
[0071] B. Subjects
[0072] The disclosed methods can be performed in any subject
capable of performing physical activity (e.g., aerobic exercise).
In some method embodiments, a subject is a living multi-cellular
vertebrate organism (e.g., human and/or non-human animals). In
other exemplary methods, a subject is a mammal (including humans
and/or non-human mammals such as veterinary or laboratory mammals)
or, in more particular examples, a racing mammal (such as a horse,
a dog, or a human). In still other methods, a subject is an adult,
an exercise-trained subject, or a healthy subject. Some
representative adult, human subjects are 16 years old or old, 18
years old or older, or 21 years old or older. Some representative
exercised-trained subjects have performed physical activity (such
described in detail above) for at least 4 weeks, for at least 6
weeks, for at least 3 months, or for at least 6 months. In some
examples the subject is healthy, for example, is a subject in which
no known disease or disorder has been diagnosed or would be
apparent after reasonable inquiry to an ordinarily skilled
physician in the field to which the disease or disorder
pertains.
[0073] C. Methods of Administration, Formulations and Dosage
[0074] The disclosed methods envision the use of any method of
administration, dosage, and/or formulation of PPAR.delta. agonist
that has the desired outcome of enhancing an exercise effect in a
subject receiving the formulation, including, without limitation,
methods of administration, dosages, and formulations well known to
those of ordinary skill in the pharmaceutical arts.
[0075] Modes of administering a PPAR.delta. agonist (or a
formulation including a PPAR.delta. agonist) in a disclosed method
include, but are not limited to, intrathecal, intradermal,
intramuscular, intraperitoneal (ip), intravenous (iv),
subcutaneous, intranasal, epidural, intradural, intracranial,
intraventricular, and oral routes. In a specific example the
PPAR.delta. agonist is administered orally. Other convenient routes
for administration of a PPAR.delta. agonist (or a formulation
including a PPAR.delta. agonist) include for example, infusion or
bolus injection, topical, absorption through epithelial or
mucocutaneous linings (for example, oral mucosa, rectal and
intestinal mucosa, and the like) ophthalmic, nasal, and
transdermal. Administration can be systemic or local. Pulmonary
administration also can be employed (for example, by an inhaler or
nebulizer), for instance using a formulation containing an
aerosolizing agent.
[0076] In specific method embodiments, it may be desirable to
administer a PPAR.delta. agonist locally. This may be achieved by,
for example, local or regional infusion or perfusion, topical
application (for example, wound dressing), injection, catheter,
suppository, or implant (for example, implants formed from porous,
non-porous, or gelatinous materials, including membranes, such as
sialastic membranes or fibers), and the like.
[0077] In other method embodiments, a pump (such as a transplanted
minipump) may be used to deliver a PPAR.delta. agonist (or a
formulation including a PPAR.delta. agonist) (see, e.g. Langer
Science 249, 1527, 1990; Sefton Crit. Rev. Biomed. Eng 14, 201,
1987; Buchwald et al., Surgery 88, 507, 1980; Saudek et al., N.
Engl. J. Med. 321, 574, 1989). In another embodiment, a PPAR.delta.
agonist (or a formulation including a PPAR.delta. agonist) is
delivered in a vesicle, in particular liposomes (see, e.g. Langer,
Science 249, 1527, 1990; Treat et al., in Liposomes in the Therapy
of Infectious Disease and Cancer, Lopez-Berestein and Fidler
(eds.), Liss, N.Y., pp. 353-365, 1989).
[0078] In yet another method embodiment, a PPAR.delta. agonist can
be delivered in a controlled-release formulation.
Controlled-release systems, such as those discussed in the review
by Langer (Science 249, 1527 1990), are known. Similarly, polymeric
materials useful in controlled-released formulations are known
(see, e.g. Ranger et al., Macromol. Sci. Rev. Macromol. Chem. 23,
61, 1983; Levy et al., Science 228, 190, 1985; During et al., Ann.
Neurol. 25, 351, 1989; Howard et al., J. Neurosurg. 71, 105, 1989).
For example, a PPAR.delta. agonists may be coupled to a class of
biodegradable polymers useful in achieving controlled release of a
compound, including polylactic acid, polyglycolic acid, copolymers
of polylactic and polyglycolic acid, polyepsilon caprolactone,
polyhydroxy butyric acid, polyorthoesters, polyacetals,
polydihydropyrans, polycyanoacrylates and cross-linked or
amphipathic block copolymers of hydrogels.
[0079] The disclosed methods contemplate the use of any dosage form
of PPAR.delta. agonist (or formulation containing the same) that
delivers the PPAR.delta. agonist and achieves a desired result.
Dosage forms are commonly known and are taught in a variety of
textbooks, including for example, Allen et al., Ansel's
Pharmaceutical Dosage Forms and Drug Delivery Systems, Eighth
Edition, Philadelphia, Pa.: Lippincott Williams & Wilkins,
2005, 738 pages. Dosage forms for use in a disclosed method
include, without limitation, solid dosage forms and solid
modified-release drug delivery systems (e.g., powders and granules,
capsules, and/or tablets); semi-solid dosage forms and transdermal
systems (e.g., ointments, creams, and/or gels); transdermal drug
delivery systems; pharmaceutical inserts (e.g., suppositories
and/or inserts); liquid dosage forms (e.g., solutions and disperse
systems); and/or sterile dosage forms and delivery systems (e.g.,
parenterals, and/or biologics). Particular exemplary dosage forms
include aerosol (including metered dose, powder, solution, and/or
without propellants); beads; capsule (including conventional,
controlled delivery, controlled release, enteric coated, and/or
sustained release); caplet; concentrate; cream; crystals; disc
(including sustained release); drops; elixir; emulsion; foam; gel
(including jelly and/or controlled release); globules; granules;
gum; implant; inhalation; injection; insert (including extended
release); liposomal; liquid (including controlled release); lotion;
lozenge; metered dose (e.g., pump); mist; mouthwash; nebulization
solution; ocular system; oil; ointment; ovules; powder (including
packet, effervescent, powder for suspension, powder for suspension
sustained release, and/or powder for solution); pellet; paste;
solution (including long acting and/or reconstituted); strip;
suppository (including sustained release); suspension (including
lente, ultre lente, reconstituted); syrup (including sustained
release); tablet (including chewable, sublingual, sustained
release, controlled release, delayed action, delayed release,
enteric coated, effervescent, film coated, rapid dissolving, slow
release); transdermal system; tincture; and/or wafer.
[0080] Typically, a dosage form is a formulation of an effective
amount (such as a therapeutically effective amount) of at least one
active pharmaceutical ingredient (such as a PPAR.delta. agonist)
with pharmaceutically acceptable excipients and/or other components
(such as one or more other active ingredients). The preferred aim
of a drug formulation is to provide proper administration of an
active ingredient (such as a PPAR.delta. agonist) to a subject. A
formulation should suit the mode of administration. The term
"pharmaceutically acceptable" means approved by a regulatory agency
of the federal or a state government or listed in the U.S.
Pharmacopoeia or other generally recognized pharmacopoeia for use
in animals, and, more particularly, in humans.
[0081] Excipients for use in exemplary formulations include, for
instance, one or more of the following: binders, fillers,
disintegrants, lubricants, coatings, sweeteners, flavors,
colorings, preservatives, diluents, adjuvants, and/or vehicles. In
some instances, excipients collectively may constitute about 5%-95%
of the total weight (and/or volume) of a particular dosage
form.
[0082] Pharmaceutical excipients can be, for instance, sterile
liquids, such as water and/or oils, including those of petroleum,
animal, vegetable, or synthetic origin, such as peanut oil, soybean
oil, mineral oil, sesame oil, and the like. Water is an exemplary
carrier when a formulation is administered intravenously. Saline
solutions, blood plasma medium, aqueous dextrose, and glycerol
solutions can also be employed as liquid carriers, particularly for
injectable solutions. Oral formulations can include, without
limitation, pharmaceutical grades of mannitol, lactose, starch,
magnesium stearate, sodium saccharine, cellulose, magnesium
carbonate, and the like. A more complete explanation of parenteral
pharmaceutical excipients can be found in Remington, The Science
and Practice of Pharmacy, 19th Edition, Philadelphia, Pa.:
Lippincott Williams & Wilkins, 1995, Chapter 95. Excipients may
also include, for example, pharmaceutically acceptable salts to
adjust the osmotic pressure, lipid carriers such as cyclodextrins,
proteins such as serum albumin, hydrophilic agents such as methyl
cellulose, detergents, buffers, preservatives and the like. Other
examples of pharmaceutical excipients include starch, glucose,
lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel,
sodium stearate, glycerol monostearate, talc, sodium chloride,
dried skim milk, glycerol, propylene, glycol, water, ethanol, and
the like. A formulation, if desired, can also contain minor amounts
of wetting or emulsifying agents, or pH buffering agents.
[0083] A dosage regimen utilizing a PPAR.delta. agonist is selected
in accordance with a variety of factors including type, species,
age, weight, sex and physical condition of the subject; the route
of administration; and/or the particular PPAR.delta. agonist
formulation employed. An ordinarily skilled physician or
veterinarian can readily determine an effective amount of a
PPAR.delta. agonist (or formulation thereof) useful for enhancing
an exercise effect in a subject.
[0084] In some method embodiments involving oral administration,
oral dosages of a PPAR.delta. agonist will generally range between
about 0.001 mg per kg of body weight per day (mg/kg/day) to about
100 mg/kg/day, and such as about 0.01-10 mg/kg/day (unless
specified otherwise, amounts of active ingredients are on the basis
of a neutral molecule, which may be a free acid or free base). For
example, an 80 kg subject would receive between about 0.08 mg/day
and 8 g/day, such as between about 0.8 mg/day and 800 mg/day. A
suitably prepared medicament for once a day administration would
thus contain between 0.08 mg and 8 g, such as between 0.8 mg and
800 mg. In some instance, formulation including a PPAR.delta.
agonist may be administered in divided doses of two, three, or four
times daily. For administration twice a day, a suitably prepared
medicament as described above would contain between 0.04 mg and 4
g, such as between 0.4 mg and 400 mg. Dosages outside of the
aforementioned ranges may be necessary in some cases. Examples of
daily dosages that may be given in the range of 0.08 mg to 8 g per
day include 0.1 mg, 0.5 mg, 1 mg, 2.5 mg, 5 mg, 10 mg, 25 mg, 50
mg, 100 mg, 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 800 mg, 1 g, 2
g, 4 g and 8 g. These amounts can be divided into smaller doses if
administered more than once per day (e.g., one-half the amount in
each administration if the drug is taken twice daily).
[0085] For some method embodiments involving administration by
injection (e.g., intravenously or subcutaneous injection), a
subject would receive an injected amount that would deliver the
active ingredient in approximately the quantities described above.
The quantities may be adjusted to account for differences in
delivery efficiency that result from injected drug forms bypassing
the digestive system. Such quantities may be administered in a
number of suitable ways, e.g. large volumes of low concentrations
of active ingredient during one extended period of time or several
times a day, low volumes of high concentrations of active
ingredient during a short period of time, e.g. once a day.
Typically, a conventional intravenous formulation may be prepared
which contains a concentration of active ingredient of between
about 0.01-1.0 mg/ml, such as for example 0.1 mg/ml, 0.3 mg/ml, or
0.6 mg/ml, and administered in amounts per day equivalent to the
amounts per day stated above. For example, an 80 kg subject,
receiving 8 ml twice a day of an intravenous formulation having a
concentration of active ingredient of 0.5 mg/ml, receives 8 mg of
active ingredient per day.
[0086] In other method embodiments, a PPAR.delta. agonist (or a
formulation thereof) can be administered at about the same dose
throughout a treatment period, in an escalating dose regimen, or in
a loading-dose regime (for example, in which the loading dose is
about two to five times a maintenance dose). In some embodiments,
the dose is varied during the course of PPAR.delta. agonist usage
based on the condition of the subject receiving the composition,
the apparent response to the composition, and/or other factors as
judged by one of ordinary skill in the art. In some embodiments
long-term administration of a PPAR.delta. agonist (or formulation
thereof) is contemplated, for instance in order to effect sustained
enhancement of an exercise effect (such as aerobic endurance, e.g.,
running endurance).
IV. Methods for Determining Drug-Induced Enhancement of Exercise
Performance
[0087] The use of performance-enhancing substances (PES),
particularly by children and professional athletes, has been in the
news because of potential adverse health consequences and the
arguable effects that such practices have on moral development of
the individual and on fair athletic competition for all (Committee
on Sports Medicine and Fitness, Reginald L. Washington, Md.,
Chairperson, Pediatrics, 115(4):1103-1106, 2005). One of the
discoveries provided herein is that certain genes (and/or the
proteins encoded thereby) are uniquely regulated by a combination
of exercise and a pharmaceutical agent (a PPAR.delta. agonist) that
results in enhanced physical performance (see Table 2). In some
cases, the particular genes (and/or proteins encoded thereby) were
up- or down-regulated by the combined treatment but were not
affected by either intervention alone. In other cases, the
particular genes (and/or proteins encoded thereby) were not
affected by the combined treatment but were up- or down-regulated
by one or both intervention when practiced alone. The unique
regulation of these genes (and/or the encoded proteins) makes them
useful markers (either alone or in any combination) for identifying
exercising subjects who are taking (or receiving) PES.
[0088] A PES is any substance taken in nonpharmacologic doses
specifically for the purpose of improving sports performance (e.g.,
by increasing strength, power, speed, or endurance (ergogenic) or
by altering body weight or body composition). Exemplary PES include
the following: (i) pharmacologic agents (prescription or
nonprescription) taken in doses that exceed the recommended
therapeutic dose or taken when the therapeutic indication(s) are
not present (e.g., using decongestants for stimulant effect, using
bronchodilators when exercise-induced bronchospasm is not present,
increasing baseline methylphenidate hydrochloride dose for athletic
competition); (ii) agents used for weight control, including
stimulants, diet pills, diuretics, and laxatives, when the user is
in a sport that has weight classifications or that rewards
leanness; (iii) agents used for weight gain, including
over-the-counter products advertised as promoting increased muscle
mass; (iv) physiologic agents or other strategies used to enhance
oxygen-carrying capacity, including erythropoietin and red blood
cell transfusions (blood doping); (v) any substance that is used
for reasons other than to treat a documented disease state or
deficiency; (vi) any substance that is known to mask adverse
effects or detectability of another performance-enhancing
substance, and/or (vii) nutritional supplements taken at
supraphysiologic doses or at levels greater than required to
replace deficits created by a disease state, training, and/or
participation in sports. In one example the PES is GW1516.
[0089] The biomarkers of substance-induced performance enhancement
identified herein and useful in a disclosed method include one or
more (or any combination of) the genes (and/or proteins encoded
thereby) listed in Table 2, and in some examples listed in Table 4.
In particular method embodiments, at least 2, at least 3, at least
5, at least 7, at least 10, at least 15, at least 20, at least 30,
or at least 40 of the genes (and/or proteins encoded thereby)
listed in Table 2 (or Table 4) are detected in a disclosed method.
In one example at least one gene (and/or protein encoded thereby)
from each class listed in Table 2 (e.g. cytokines, fat metabolism)
is analyzed.
[0090] In more specific method embodiments, upregulated expression
is detected for one or more of the following genes (or proteins
encoded thereby): adipose differentiation related protein;
stearoyl-Coenzyme A desaturase 2; acetyl-Coenzyme A
acetyltransferase 2; ATP citrate lyase; adiponectin, C1Q and
collagen domain containing; diacylglycerol O-acyltransferase 2;
lipase, hormone sensitive; monoglyceride lipase; resistin; CD36
antigen; fatty acid binding protein 4, adipocyte; lipoprotein
lipase; microsomal glutathione S-transferase 1; GPI-anchored
membrane protein 1; dual specificity phosphatase 7; homeodomain
interacting protein kinase 3; insulin-like growth factor binding
protein 5; protein phosphatase 2 (formerly 2A), regulatory subunit
A (PR 65), beta isoform; protein tyrosine phosphatase-like (proline
instead of catalytic arginine); member b; CCAAT/enhancer binding
protein (C/EBP), alpha; nuclear receptor subfamily 1, group D,
member 2(Reverb-b); transferring; archain 1; solute carrier family
1 (neutral amino acid transporter), member 5; RIKEN cDNA 1810073N04
gene; haptoglobin; retinol binding protein 4, plasma;
phosphoenolpyruvate carboxykinase 1, cytosolic; cell death-inducing
DFFA-like effector c; interferon, alpha-inducible protein 27;
carbonic anhydrase 3; cysteine dioxygenase 1, cytosolic; DNA
segment, Chr 4, Wayne State University 53, expressed; dynein
cytoplasmic 1 intermediate chain 2; Kruppel-like factor 3 (basic);
thyroid hormone responsive SPOT14 homolog (Rattus); cytochrome
P450, family 2, subfamily e, polypeptide 1; complement factor D
(adipsin); and/or transketolase. In particular method embodiments,
upregulation of at least 2, at least 3, at least 5, at least 7, at
least 10, at least 15, at least 20, at least 30, or at least 38 of
the foregoing genes (and/or proteins encoded thereby) are detected
in a disclosed method.
[0091] In other method embodiments, downregulated expression is
detected in one or more of the following genes (and/or proteins
encoded thereby): gamma-glutamyl carboxylase; 3-oxoacid CoA
transferase 1; solute carrier family 38, member 4; annexin A7; CD55
antigen; RIKEN cDNA 1190002H23 gene; fusion, derived from t(12;16)
malignant liposarcoma (human); lysosomal membrane glycoprotein 2;
and/or neighbor of Punc E11. In particular method embodiments,
downregulation of at least 2, at least 3, at least 5, or at least 7
of the foregoing genes (and/or proteins encoded thereby) are
detected in a disclosed method.
[0092] In still other method embodiments, a combination of
upregulated genes (and/or proteins encoded thereby) and
downregulated genes (and/or proteins encoded thereby) as described
above is detected in a sample from a subject (such as, an exercised
or exercise-trained subject).
[0093] Yet other method embodiments involve the detection in a
sample of a combination of the above-described upregulated genes
(and/or proteins encoded thereby) and/or the above-described
downregulated genes (and/or proteins encoded thereby), and/or the
above-described exercise-regulated genes that are not affected by
exercise combined with PPAR.delta. administration.
[0094] Disclosed methods may be used for detecting PES use in any
subject capable of taking or receiving one or more such PES. In
some method embodiments, a subject is a living multi-cellular
vertebrate organism (e.g., human and/or non-human animals). In
other exemplary methods, a subject is a mammal (including humans
and/or non-human mammals) or, in more particular examples, a racing
mammal (such as a horse, a dog, or a human). In still other
methods, a subject is an exercise-trained subject. Some
representative exercised-trained subjects have performed physical
activity (such described in detail above) for at least 4 weeks, for
at least 6 weeks, for at least 3 months, or for at least 6 months.
Other exercise-trained subjects may be student athletes and/or
professional athletes (including, in some examples, non-human
professional athletes, such as race horses and/or racing dogs).
[0095] Any sample from a subject (e.g., a biological sample) in
which can be detected one or more genes and/or proteins uniquely
regulated by exercise in combination with PPAR.delta. agonist
intake (as described in detail throughout this specification) is
contemplated for use in a disclosed method. Exemplary samples for
use in a disclosed method include blood, saliva, urine, muscle
biopsy (e.g., skeletal muscle biopsy), cheek swab, fecal sample,
sweat, and/or sperm.
[0096] Methods of detecting the expression of genes and/or proteins
in a sample (e.g, biological sample) are very well known (see,
e.g., U.S. Pat. Nos. 6,911,307; 6,893,824; 5,972,692; 5,972,602;
5,776,672; 7,031,847; 6,816,790; 6,811,977; 6,806,049; 6,203,988;
and/or 6,090,556).
[0097] In particular method embodiments, expression of one or more
genes identified herein can be detected by any method of nucleic
acid amplification (such as, polymerase chain reaction (PCR) or any
adaptation thereof, ligase chain reaction, transcription-based
amplification systems, cycling probe reaction, Q.beta. replicase
amplification, strand displacement amplification, and/or rolling
circle amplification), solid-surface hybridization assays (such as
Northern blot, dot blot, gene chips, and/or reversible target
capture), solution hybridization assays (such as MAP technology
(which uses a liquid suspension array of 100 sets of 5.5 micron
probe-conjugated beads, each internally dyed with different ratios
of two spectrally distinct fluorophores to assign it a unique
spectral address)), and/or in situ hybridization. Various of the
foregoing nucleic acid detection methods are described in detail in
the review by Wolcott (Clin. Microbiol. Rev., 5(4):370-386, 1992).
Other detailed and long-established protocols for practicing some
such nucleic acid detection methods are found in Sambrook et al.,
Molecular Cloning: A Laboratory Manual, 2nd edition, Cold Spring
Harbor Laboratory Press, 1989; Sambrook et al., Molecular Cloning:
A Laboratory Manual, 3rd edition, Cold Spring Harbor Press, 2001;
Ausubel et al., Current Protocols in Molecular Biology, Greene
Publishing Associates, 1992 (and Supplements to 2000); and/or
Ausubel et al., Short Protocols in Molecular Biology: A Compendium
of Methods from Current Protocols in Molecular Biology, 4th
edition, Wiley & Sons, 1999.
[0098] In other method embodiments, expression of one or more
proteins encoded by corresponding genes identified herein can be
detected by Western blot, immunohistochemistry,
immunoprecipitation, antibody microarrays, ELISA, and/or by
functional assay (e.g., kinase assay, ATPase assay, substrate (or
ligand) binding assay, protein-protein binding assay, or other
assay suitable for measuring a particular protein function).
[0099] If the pattern of expression identified in the test subject
is similar to that shown in Table 2 (e.g. the genes shown as
upregulated and downregulated in Table 2 are observed in the
subject to be upregulated and downregulated, respectively), this
indicates that the subject is taking a PES, such as a PPAR.delta.
agonist (e.g. GW1516). In contrast, If the pattern of expression
identified in the test subject is different to that shown in Table
2 (e.g. the genes shown as upregulated and downregulated in Table 2
are observed in the subject to be not differentially expressed or
show a different pattern of regulation), this indicates that the
subject is not taking a PES, such as a PPAR.delta. agonist (e.g.
GW1516).
V. Methods for Identifying Agents of Potential Interest
[0100] This disclosure identifies a previously unknown
protein-protein interaction between PPAR.delta. and particular
exercise-induced kinases (e.g., AMPK, such as the AMPK.alpha.1
and/or AMPK.alpha.2 subunit(s) of AMPK). The interaction between
PPAR.delta. and AMPK may have important functional outcomes, such
as enhancing exercise performance (e.g., aerobic exercise
performance, such as running endurance) in a subject.
[0101] The foregoing discoveries enable methods for identify
agents, e.g., having potential to enhance exercise performance
(e.g., aerobic exercise performance, such as running endurance) in
a subject. In some such methods, agents that affect (e.g., enhance,
weaken, or substantially disrupt) the protein-protein interaction
are identified. In other such methods, agents that affect (e.g.,
increase, decrease, or substantially eliminate) AMPK-dependent
phosphorylation of a PPAR.delta. complex are identified.
[0102] A. Exemplary Agents
[0103] An "agent" is any substance or any combination of substances
that is useful for achieving an end or result; for example, a
substance or combination of substances useful for modulating a
protein activity (e.g., AMPK-dependent phosphorylation of a
PPAR.delta. complex), or useful for modifying or affecting a
protein-protein interaction (e.g., PPAR.delta.-AMPK interaction).
Any agent that has potential (whether or not ultimately realized)
to modulate any aspect of the PPAR.delta.-AMPK interaction
disclosed herein is contemplated for use in the screening methods
of this disclosure.
[0104] Exemplary agents include, but are not limited to, peptides
such as, for example, soluble peptides, including but not limited
to members of random peptide libraries (see, e.g. Lam et al.,
Nature, 354:82-84, 1991; Houghten et al., Nature, 354:84-86, 1991),
and combinatorial chemistry-derived molecular library made of D-
and/or L-configuration amino acids, phosphopeptides (including, but
not limited to, members of random or partially degenerate, directed
phosphopeptide libraries; see, e.g. Songyang et al., Cell,
72:767-778, 1993), antibodies (including, but not limited to,
polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or
single chain antibodies, and Fab, F(ab').sub.2 and Fab expression
library fragments, epitope-binding fragments thereof), small
organic or inorganic molecules (such as, so-called natural products
or members of chemical combinatorial libraries), molecular
complexes (such as protein complexes), or nucleic acids.
[0105] Libraries (such as combinatorial chemical libraries) useful
in the disclosed methods include, but are not limited to, peptide
libraries (see, e.g. U.S. Pat. No. 5,010,175; Furka, Int. J. Pept.
Prot. Res., 37:487-493, 1991; Houghton et al., Nature, 354:84-88,
1991; PCT Publication No. WO 91/19735), encoded peptides (e.g. PCT
Publication WO 93/20242), random bio-oligomers (e.g. PCT
Publication No. WO 92/00091), benzodiazepines (e.g. U.S. Pat. No.
5,288,514), diversomers such as hydantoins, benzodiazepines and
dipeptides (Hobbs et al., Proc. Natl. Acad. Sci. USA, 90:6909-6913,
1993), vinylogous polypeptides (Hagihara et al., J. Am. Chem. Soc.,
114:6568, 1992), nonpeptidal peptidomimetics with glucose
scaffolding (Hirschmann et al., J. Am. Chem. Soc., 114:9217-9218,
1992), analogous organic syntheses of small compound libraries
(Chen et al., J. Am. Chem. Soc., 116:2661, 1994), oligocarbamates
(Cho et al., Science, 261: 1303, 1003), and/or peptidyl
phosphonates (Campbell et al., J. Org. Chem., 59:658, 1994),
nucleic acid libraries (see Sambrook et al. Molecular Cloning, A
Laboratory Manual, Cold Springs Harbor Press, N.Y., 1989; Ausubel
et al., Current Protocols in Molecular Biology, Green Publishing
Associates and Wiley Interscience, N.Y., 1989), peptide nucleic
acid libraries (see, e.g. U.S. Pat. No. 5,539,083), antibody
libraries (see, e.g. Vaughn et al., Nat. Biotechnol., 14:309-314,
1996; PCT App. No. PCT/US96/10287), carbohydrate libraries (see,
e.g. Liang et al., Science, 274:1520-1522, 1996; U.S. Pat. No.
5,593,853), small organic molecule libraries (see, e.g.
benzodiazepines, Baum, C&EN, January 18, page 33, 1993;
isoprenoids, U.S. Pat. No. 5,569,588; thiazolidionones and
methathiazones, U.S. Pat. No. 5,549,974; pyrrolidines, U.S. Pat.
Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Pat. No.
5,506,337; benzodiazepines, U.S. Pat. No. 5,288,514) and the
like.
[0106] Libraries useful for the disclosed screening methods can be
produce in a variety of manners including, but not limited to,
spatially arrayed multipin peptide synthesis (Geysen, et al., Proc.
Natl. Acad. Sci., 81(13):3998-4002, 1984), "tea bag" peptide
synthesis (Houghten, Proc. Natl. Acad. Sci., 82(15):5131-5135,
1985), phage display (Scott and Smith, Science, 249:386-390, 1990),
spot or disc synthesis (Dittrich et al., Bioorg. Med. Chem. Lett.,
8(17):2351-2356, 1998), or split and mix solid phase synthesis on
beads (Furka et al., Int. J. Pept. Protein Res., 37(6):487-493,
1991; Lam et al., Chem. Rev., 97(2):411-448, 1997).
[0107] Libraries may include a varying number of compositions
(members), such as up to about 100 members, such as up to about
1000 members, such as up to about 5000 members, such as up to about
10,000 members, such as up to about 100,000 members, such as up to
about 500,000 members, or even more than 500,000 members.
[0108] In one convenient embodiment, high throughput screening
methods involve providing a combinatorial chemical or peptide
library containing a large number of potential therapeutic
compounds (e.g., affectors of AMPK-PPAR.delta. protein-protein
interactions). Such combinatorial libraries are then screened in
one or more assays as described herein to identify those library
members (particularly chemical species or subclasses) that display
a desired characteristic activity (such as increasing or decreasing
an AMPK-PPAR.delta. protein-protein interaction). The compounds
thus identified can serve as conventional "lead compounds" or can
themselves be used as potential or actual therapeutics. In some
instances, pools of candidate agents may be identify and further
screened to determine which individual or subpools of agents in the
collective have a desired activity.
[0109] B. Exemplary Assays
[0110] As disclosed herein, PPAR.delta. forms a protein-protein
interaction with AMPK or one or more of its subunits (such as
AMPK.alpha.1 and/or AMPK.alpha.2). Agents that affect (e.g.,
increase or decrease) an AMPK-PPAR.delta. interaction or
AMP-dependent phosphorylation of a PPAR.delta. complex may have the
effect of enhancing exercise performance (e.g., aerobic exercise
performance, such as running endurance) in a subject and,
therefore, are desirable to identify.
[0111] In screening methods described here, tissue samples,
isolated cells, isolated polypeptides, and/or test agents can be
presented in a manner suitable for high-throughput screening; for
example, one or a plurality of isolated tissue samples, isolated
cells, or isolated polypeptides can be inserted into wells of a
microtitre plate, and one or a plurality of test agents can be
added to the wells of the microtitre plate. Alternatively, one or a
plurality of test agents can be presented in a high-throughput
format, such as in wells of microtitre plate (either in solution or
adhered to the surface of the plate), and contacted with one or a
plurality of isolated tissue samples, isolated cells, and/or
isolated polypeptides under conditions that, at least, sustain the
tissue sample or isolated cells or a desired polypeptide function
and/or structure. Test agents can be added to tissue samples,
isolated cells, or isolated polypeptides at any concentration that
is not lethal to tissues or cells, or does not have an adverse
effect on polypeptide structure and/or function. It is expected
that different test agents will have different effective
concentrations. Thus, in some methods, it is advantageous to test a
range of test agent concentrations.
[0112] Disclosed methods envision, as appropriate, the use of
PPAR.delta. or AMPK (such as AMPK.alpha.1 or AMPK.alpha.2) or
functional fragments of any thereof as contained, independently, in
a subject, one or a plurality of cells or cellular extracts, one or
a plurality of tissue or tissue extracts, or as an isolated
polypeptide. PPAR.delta. ligand optionally is included (or is
omitted) in disclosed methods.
[0113] 1. Agents that Affect a Protein-Protein Interaction
[0114] A "direct association" between two or more polypeptides
(such as, PPAR.delta. and AMPK (such as AMPK.alpha.1 or
AMPK.alpha.2) is characterized by physical contact between at least
a portion of the interacting polypeptides that is of sufficient
affinity and specificity that, for example, immunoprecipitation of
one of the polypeptides also will specifically precipitate the
other polypeptide; provided that the immunoprecipitating antibody
does not also affect the site(s) involved in the interaction. A
direct association between polypeptides also may be referred to as
a "protein-protein interaction." The binding of one polypeptide to
another in a protein-protein interaction (e.g., PPAR.delta. to AMPK
(or AMPK.alpha.1 and/or AMPK.alpha.2) and vice versa) is considered
"specific binding".
[0115] Agents that affect an AMPK-PPAR.delta. interaction can be
identified by a variety of assays, including solid-phase or
solution-based assays. In an exemplary solid-phase assay,
PPAR.delta. or an AMPK-binding fragment thereof and AMPK or a
subunit thereof (such as AMPK.alpha.1 and/or AMPK.alpha.2) or a
PPAR.delta.-binding fragment thereof are mixed under conditions in
which PPAR.delta. and AMPK (or its subunit(s) or functional
fragments) normally interact (e.g., co-immunoprecipitate). One of
the binding partners is labeled with a marker such as biotin,
fluoroscein, EGFP, or enzymes to allow easy detection of the
labeled component. The unlabeled binding partner is adsorbed to a
support, such as a microtiter well or beads. Then, the labeled
binding partner is added to the environment where the unlabeled
binding partner is immobilized under conditions suitable for
interaction between the two binding partners. One or more test
compounds, such as compounds in one or more of the above-described
libraries, are separately added to individual microenvironments
containing the interacting binding partners. Agents capable of
affecting the interaction between the binding partners are
identified, for instance, as those that increase or decrease (e.g.,
increase) retention or binding of the signal (i.e., labeled binding
partner) in the reaction microenvironment, for example, in a
microtiter well or on a bead for example. As discussed previously,
combinations of agents can be evaluated in an initial screen to
identify pools of agents to be tested individually, and this
process is easily automated with currently available
technology.
[0116] In other method embodiments, solution phase selection can be
used to screen large complex libraries for agents that specifically
affect protein-protein interactions (see, e.g., Boger et al.,
Bioorg. Med. Chem. Lett., 8(17):2339-2344, 1998); Berg et al.,
Proc. Natl. Acad. Sci., 99(6):3830-3835, 2002). In one such
example, each of two proteins that are capable of physical
interaction (for example, PPAR.delta. (or AMPK-binding fragments
thereof) and AMPK or AMPK.alpha.1 or AMPK.alpha.2 (or
PPAR.delta.-binding fragments of any thereof) are labeled with
fluorescent dye molecule tags with different emission spectra and
overlapping adsorption spectra. When these protein components are
separate, the emission spectrum for each component is distinct and
can be measured. When the protein components interact, fluorescence
resonance energy transfer (FRET) occurs resulting in the transfer
of energy from a donor dye molecule to an acceptor dye molecule
without emission of a photon. The acceptor dye molecule alone emits
photons (light) of a characteristic wavelength. Therefore, FRET
allows one to determine the kinetics of two interacting molecules
based on the emission spectra of the sample. Using this system, two
labeled protein components are added under conditions where their
interaction resulting in FRET emission spectra. Then, one or more
test compounds, such as compounds in one or more of the
above-described libraries, are added to the environment of the two
labeled protein component mixture and emission spectra are
measured. An increase in the FRET emission, with a concurrent
decrease in the emission spectra of the separated components
indicates that an agent (or pool of candidate agents) has affected
(e.g., enhanced) the interaction between the protein
components.
[0117] Interactions between PPAR.delta. (or AMPK-binding fragments
thereof) and AMPK or AMPK.alpha.1 or AMPK.alpha.2 (or
PPAR.delta.-binding fragments of any thereof) also can be
determined (e.g., quantified) by co-immunoprecipitation of the
relevant component polypeptides (e.g. from cellular extracts), by
GST-pull down assay (e.g., using purified GST-tagged bacterial
proteins), and/or by yeast two-hybrid assay, each of which methods
is standard in the art. Conducting any one or more such assays in
the presence and, optionally, absence of a test compound can be
used to identify agents that improve or enhance (or, in other
embodiments, decrease or inhibit) the interaction between
PPAR.delta. (or AMPK-binding fragments thereof) and AMPK or
AMPK.alpha.1 or AMPK.alpha.2 (or PPAR.delta.-binding fragments of
any thereof) in the presence of a test compound as compared to in
the absence of the test compound or as compared to some other
standard or control.
[0118] In certain method embodiments, one or more AMPK (such as
AMPK.alpha.1 and/or AMPK.alpha.2)-binding fragments of PPAR.delta.
and/or one or more PPAR.delta.-binding fragments of AMPK (such as
AMPK.alpha.1 and/or AMPK.alpha.2) are used. Polypeptide fragments
having the desired binding activities can be identified by making a
series of defined PPAR.delta. fragments and/or AMPK (such as
AMPK.alpha.1 or AMPK.alpha.2) fragments using methods standard in
the art. For example, cDNA encoding the protein(s) of interest
(e.g., PPAR.delta. or AMPK) can be serially truncated from the 3'
or 5' end (provided that a start codon is engineered into 5'
truncations) using conveniently located restriction enzyme sites
(or other methods) and leaving intact (or otherwise correcting) the
proper reading frame. Conveniently, a nucleic acid sequence
encoding an epitope tag (such as a FLAG tag) is placed in frame
with (and substantially adjacent to) the truncated protein-encoding
sequence to produce a nucleic acid sequence encoding an
epitope-tagged protein fragment. The epitope-tagged protein
fragment can be expressed in any convenient expression system (such
as a bacterial expression system), isolated or not, and mixed with
a sample containing a protein or other protein fragment to which
the epitope-tagged protein fragment may bind. An antibody specific
for the tag (or other region of the protein fragment) can be used
to immunoprecipitate the fragment of interest together with any
protein(s) or protein fragment(s) that bind to it. Protein(s) or
protein fragment(s) that bind to the epitope-tagged protein
fragment of interest can be particular identified, e.g., by Western
blot.
[0119] In particular methods, the formation of a PPAR.delta.-AMPK
(such as AMPK.alpha.1 and/or AMPK.alpha.2) complex (including
complexes including one or both of PPAR.delta.-binding AMPK
fragments and/or AMPK-binding PPAR.delta. fragments) or the
affinity of PPAR.delta. (or AMPK-binding fragments thereof) and
AMPK (or PPAR.delta.-binding fragments thereof) for each other is
increased when the amount of such complex or the binding affinity
is at least 5%, at least 10%, at least 20%, at least 30%, at least
50%, at least 100% or at least 250% higher than a control
measurement (e.g., in the same test system prior to addition of a
test agent, or in a comparable test system in the absence of a test
agent).
[0120] In other particular methods, the formation of a
PPAR.delta.-AMPK (such as AMPK.alpha.1 and/or AMPK.alpha.2) complex
(including complexes including one or both of PPAR.delta.-binding
AMPK fragments and/or AMPK-binding PPAR.delta. fragments) or the
affinity of PPAR.delta. (or AMPK-binding fragments thereof) and
AMPK (or PPAR.delta.-binding fragments thereof) for each other is
decreased when the amount of such complex or the binding affinity
is at least 5%, at least 10%, at least 20%, at least 30%, at least
50%, at least 100% or at least 250% lower than a control
measurement (e.g., in the same test system prior to addition of a
test agent, or in a comparable test system in the absence of a test
agent).
[0121] 2. Agents that Affect AMPK-Dependent Phosyphorylation
[0122] Disclosed are methods of screening test agents for those
that affect (e.g., increase or decrease) AMPK (e.g., AMPK.alpha.1
and/or AMPK.alpha.2)-dependent phosphorylation of the PPAR.delta.
complex. Agents that affect AMPK-dependent phosphorylation of the
PPAR.delta. complex can be identified by a variety of assays, such
adaptations of solid-phase- or solution-based assays described
above, where the end point to be detected is phosphorylation of one
or more components of the PPAR.delta. complex.
[0123] Methods for detecting protein phosphorylation are
conventional (see, e.g., Gloffke, The Scientist, 16(19):52, 2002;
Screaton et al., Cell, 119:61-74, 2004) and detection kits are
available from a variety of commercial sources (see, e.g., Upstate
(Charlottesville, Va., USA), Bio-Rad (Hercules, Calif., USA),
Marligen Biosciences, Inc. (Ijamsville, Md., USA), Calbiochem (San
Diego, Calif., USA). Briefly, phosphorylated protein (e.g.,
phosphorylation of one or more components of the PPAR.delta.
complex) can be detected using stains specific for phosphorylated
proteins in gels. Alternatively, antibodies specific phosphorylated
proteins can be made or commercially obtained. Antibodies specific
for phosphorylated proteins can be, among other things, tethered to
the beads (including beads having a particular color signature) or
used in ELISA or Western blot assays.
[0124] In one example, a PPAR.delta. complex (or a fragment thereof
containing an AMPK phosphorylation site) and AMPK or one or more of
it subunits (such as AMPK.alpha.1 and/or AMPK.alpha.2) or
functional fragments thereof that are capable of phosphorylation
are mixed under conditions whereby a PPAR.delta. complex is
phosphorylated by AMPK. A PPAR.delta. complex is adsorbed to a
support, such as a microtiter well or beads. Then, AMPK (or its one
or more subunits (such as AMPK.alpha.1 and/or AMPK.alpha.2) or
phosphorylation-capable fragments thereof) is added to the
environment where the complex is immobilized. A phosphate donor
typically is also included in the environment. The phosphate to be
donated, optionally, can be labeled. One or more test compounds,
such as compounds in one or more of the above-described libraries,
are separately added to the individual microenvironments. Agents
capable of affecting AMPK-dependent phosphorylation are identified,
for instance, as those that enhance (or inhibit) phosphorylation of
immobilized PPAR.delta. complex. In embodiments involving a labeled
phosphate donor, phosphorylation of immobilized PPAR.delta. complex
can be determined by retention or binding of a labeled phosphate in
the reaction microenvironment, for example, in a microtiter well or
on a bead for example. In other embodiments, such reactions can
take place in solution (i.e., with no immobilized components),
PPAR.delta. complex can be isolated from the solution (e.g., by
immunoprecipitation with PPAR.delta.-specific or phosphate-specific
antibodies), and its level of phosphorylation in the presence (and,
optionally, absence) of one of more test agents determined as
previously discussed.
[0125] In particular methods, the phosphorylation of a PPAR.delta.
complex is increased when such posttranslational modification is
detectably measured or when such posttranslational modification is
at least 20%, at least 30%, at least 50%, at least 100% or at least
250% higher than control measurements (e.g., in the same test
system prior to addition of a test agent, or in a comparable test
system in the absence of a test agent, or in a comparable test
system in the absence of AMPK).
[0126] In particular methods, the phosphorylation of PPAR.delta.
complex is decreased when such posttranslational modification is
detectably reduced or when such posttranslational modification is
at least 20%, at least 30%, at least 50%, at least 100% or at least
250% lower than control measurements (e.g., in the same test system
prior to addition of a test agent, or in a comparable test system
in the absence of a test agent, or in a comparable test system in
the absence of AMPK).
[0127] C. Screening Assay Target(s)
[0128] 1. PPAR.delta.
[0129] A PPAR.delta. polypeptide useful in a disclosed screening
method is any known PPAR.delta. receptor. Also useful in the
disclosed screening methods are homologs, functional fragments, or
functional variants of a PPAR.delta. that retains at least
AMPK-binding activity as described herein for a prototypical
PPAR.delta. polypeptide (see Example 6).
[0130] The amino acid sequences of prototypical PPAR.delta.
polypeptides (and PPAR.delta.-encoding nucleic acid sequences) are
well known. Exemplary PPAR.delta. amino acid sequences and
PPAR.delta.-encoding nucleic acid sequences are described, for
instance, in U.S. Pat. No. 5,861,274, and U.S. Pat. Appl. Pub. No.
20060154335 (each of which is expressly incorporated herein by
reference), and in GenBank Accession Nos. NP.sub.--035275
(GI:33859590)(Mus musculus amino acid sequence); NM.sub.--011145.3
(GI:89001112)(Mus musculus nucleic acid sequence); NP.sub.--006229
(GI:5453940)(Homo sapiens amino acid sequence); NM 006238.3
(GI:89886454)(Homo sapiens nucleic acid sequence); NP.sub.--037273
(GI:6981384)(Rattus norvegicus amino acid sequence);
NM.sub.--013141.1 (GI:6981383)(Rattus norvegicus nucleic acid
sequence); NP.sub.--990059 (gi45382025)(Gallus gallus amino acid
sequence) or NM.sub.--204728.1 (GI:45382024)(Gallus gallus nucleic
acid sequence). In some method embodiments, a PPAR.delta. homolog
or functional variant shares at least 60% amino acid sequence
identity with a prototypical PPAR.delta. polypeptide; for example,
at least 75%, at least 80%, at least 85%, at least 90%, at least
95%, or at least 98% amino acid sequence identity with an amino
acid sequence as set forth in U.S. Pat. No. 5,861,274, U.S. Pat.
Appl. Pub. No. 20060154335, or GenBank Accession No.
NP.sub.--035275 (GI:33859590)(Mus musculus amino acid sequence);
NP.sub.--006229 (GI:5453940)(Homo sapiens amino acid sequence);
NP.sub.--037273 (GI:6981384)(Rattus norvegicus amino acid
sequence); or NP.sub.--990059 (gi45382025) (Gallus gallus amino
acid sequence). In other method embodiments, a PPAR.delta. homolog
or functional variant has one or more conservative amino acid
substitutions as compared to with a prototypical PPAR.delta.
polypeptide; for example, no more than 3, 5, 10, 15, 20, 25, 30,
40, or 50 conservative amino acid changes compared to an amino acid
sequence as set forth in U.S. Pat. No. 5,861,274, U.S. Pat. Appl.
Pub. No. 20060154335, or GenBank Accession No. NP.sub.--035275
(GI:33859590)(Mus musculus amino acid sequence); NP.sub.--006229
(GI:5453940)(Homo sapiens amino acid sequence); NP.sub.--037273
(GI:6981384)(Rattus norvegicus amino acid sequence); or
NP.sub.--990059 (gi45382025)(Gallus gallus amino acid sequence).
The following table shows exemplary conservative amino acid
substitutions:
TABLE-US-00001 Conservative Original Residue Substitutions Ala Ser
Arg Lys Asn Gln; His Asp Glu Cys Ser Gln Asn Glu Asp Gly Pro His
Asn; Gln Ile Leu; Val Leu Ile; Val Lys Arg; Gln; Glu Met Leu; Ile
Phe Met; Leu; Tyr Ser Thr Thr Ser Trp Tyr Tyr Trp; Phe Val Ile;
Leu
[0131] Some method embodiments involve a PPAR.delta. functional
fragment (such as an AMPK-binding fragment), which can be any
portion of a full-length known PPAR.delta. polypeptide, including,
e.g., about 20, about 30, about 40, about 50, about 75, about 100,
about 150 or about 200 contiguous amino acid residues of same;
provided that the fragment retains a PPAR.delta. function of
interest (e.g., AMPK binding). PPAR.delta. encompasses known
functional motifs (such as ligand-binding domain, a DNA-binding
domain, and a transactivation domain).
[0132] 2. AMPK
[0133] Mammalian AMP-activated kinase (AMPK) is a heterotrimeric
protein composed of 1 alpha subunit, 1 beta subunit, and 1 gamma
subunit. There are, at least, two known isoforms of the alpha
subunit (.alpha.1 and a2). AMPK.alpha.1 and AMPK.alpha.2 have 90%
amino acid sequence identity within their catalytic cores but only
61% in their C-terminal tails (see Online Mendelian Inheritance in
Man (OMIM) Database Accession No. 602739; publicly available at the
following website:
ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602739).
[0134] An AMPK (such as AMPK.alpha.1 and/or AMPK.alpha.2)
polypeptide useful in a disclosed screening method is any known
AMPK protein or subunit thereof (such as AMPK.alpha.1 and/or
AMPK.alpha.2). Also useful in the disclosed screening methods are
homologs, functional fragments, or functional variants of an AMPK
protein or subunit thereof (such as AMPK.alpha.1 and/or
AMPK.alpha.2) that retains at least PPAR.delta.-binding activity as
described herein (see Example 6).
[0135] The amino acid sequences of prototypical AMPK subunits (such
as AMPK.alpha.1 and/or AMPK.alpha.2) (and nucleic acids sequences
encoding prototypical AMPK subunits (such as AMPK.alpha.1 and/or
AMPK.alpha.2)) are well known. Exemplary AMPK.alpha.1 amino acid
sequences and the corresponding nucleic acid sequences are
described, for instance, in GenBank Accession Nos.
NM.sub.--206907.3 (GI:94557298)(Homo sapiens transcript variant 2
REFSEQ including amino acid and nucleic acid sequences);
NM.sub.--006251.5 (GI:94557300)(Homo sapiens transcript variant 1
REFSEQ including amino acid and nucleic acid sequences);
NM.sub.--001013367.3 (GI:94681060)(Mus musculus REFSEQ including
amino acid and nucleic acid sequences); NM.sub.--001039603.1
(GI:88853844)(Gallus gallus REFSEQ including amino acid and nucleic
acid sequences); and NM 019142.1 (GI: 11862979)(Rattus norvegicus
REFSEQ including amino acid and nucleic acid sequences). Exemplary
AMPK.alpha.2 amino acid sequences and the corresponding nucleic
acid sequences are described, for instance, in GenBank Accession
Nos. NM.sub.--006252.2 (GI:46877067)(Homo sapiens REFSEQ including
amino acid and nucleic acid sequences); NM.sub.--178143.1
(GI:54792085)(Mus musculus REFSEQ including amino acid and nucleic
acid sequences); NM.sub.--001039605.1 (GI:88853850) (Gallus gallus
REFSEQ including amino acid and nucleic acid sequences); and
NM.sub.--214266.1 (GI:47523597)(Sus scrofa REFSEQ including amino
acid and nucleic acid sequences).
[0136] In some method embodiments, a homolog or functional variant
of an AMPK subunit shares at least 60% amino acid sequence identity
with a prototypical AMPK.alpha.1 and/or AMPK.alpha.2 polypeptide;
for example, at least 75%, at least 80%, at least 85%, at least
90%, at least 95%, or at least 98% amino acid sequence identity
with an amino acid sequence as set forth in the GenBank Accession
Nos. NM 206907.3; NM.sub.--006251.5; NM.sub.--001013367.3;
NM.sub.--001039603.1; NM.sub.--019142.1; NM.sub.--006252.2;
NM.sub.--178143.1; NM.sub.--001039605.1; or NM.sub.--214266.1. In
other method embodiments, a homolog or functional variant of an
AMPK subunit has one or more conservative amino acid substitutions
as compared to a prototypical AMPK.alpha.1 and/or AMPK.alpha.2
polypeptide; for example, no more than 3, 5, 10, 15, 20, 25, 30,
40, or 50 conservative amino acid changes compared to an amino acid
sequence as set forth in as set forth in GenBank Accession Nos. NM
206907.3; NM.sub.--006251.5; NM.sub.--001013367.3;
NM.sub.--001039603.1; NM.sub.--019142.1; NM.sub.--006252.2;
NM.sub.--178143.1; NM.sub.--001039605.1; or NM.sub.--214266.1.
Exemplary conservative amino acid substitutions have been
previously described herein.
[0137] Some method embodiments involve a functional fragment of
AMPK or a subunit thereof (such as AMPK.alpha.1 and/or
AMPK.alpha.2), including a PPAR.delta.-binding fragment or a
fragment with PPAR.delta. phosphorylation activity. Functional
fragments of AMPK or a subunit thereof (such as AMPK.alpha.1 and/or
AMPK.alpha.2) can be any portion of a full-length or intact AMPK
polypeptide complex or subunit thereof (such as AMPK.alpha.1 and/or
AMPK.alpha.2), including, e.g., about 20, about 30, about 40, about
50, about 75, about 100, about 150 or about 200 contiguous amino
acid residues of same; provided that the fragment retains at least
one AMPK (or AMPK.alpha.1 and/or AMPK.alpha.2) function of interest
(e.g., PPAR.delta. binding and/or PPAR.delta. phosphorylation
activity). Protein-protein interactions between PPAR.delta. and
AMPK are believed to involve, at least, an AMPKA subunit (such as
AMPK.alpha.1 and/or AMPK.alpha.2). Moreover, because PPAR.delta.
specifically binds both AMPK.alpha.1 and AMPK.alpha.2 (see Example
6), such interaction likely is mediated by the portions of these
AMPKA isoforms that share the most sequence homology (as discussed
above). Accordingly, in some method embodiments, an AMPK
PPAR.delta.-binding fragment includes a functional fragment
encompassing (or consisting of) the catalytic core domain of an
alpha subunit of AMPK (such as AMPK.alpha.1 and/or
AMPK.alpha.2).
EXAMPLES
[0138] The following examples are provided to illustrate certain
particular features and/or embodiments. These examples should not
be construed to limit the invention to the particular features or
embodiments described.
Example 1
Administration of PPAR.delta. Agonist Surprisingly does not Enhance
Physical Performance in Non-Exercised Subjects
[0139] Wang et al. previously demonstrated that skeletal
muscle-specific expression of a constitutively active form of
PPAR.delta. receptor resulted in transgenic mice with skeletal
muscles that had an increased number of slow, oxidative (type I)
muscle fibers and markedly increased running endurance (Wang et
al., PLoS Biol., 2:e294, 2004). This Example demonstrates that
administration of a PPAR.delta. agonist (GW1516) to non-transgenic
mice also results in the expression in skeletal muscle of some
biomarkers of oxidative metabolism. However, in unexpected contrast
to the results obtained by genetic activation of the PPAR.delta.
pathway, PPAR.delta. activation by pharmacological treatment did
not modify fiber-type composition of skeletal muscle, nor improve
running endurance in non-transgenic, sedentary (also referred to as
"non-exercised" or "untrained") mice.
[0140] Male C57B/6J mice (8 wks old) were obtained from Jackson
Laboratory and housed in the Salk Institute animal care facility.
The animals were acclimated to their surroundings for one week
prior to experimentation, and had access at all times to standard
mouse chow and water ad libitum.
[0141] Mice were acclimated to moderate treadmill running (10 m/min
for 15 min) every other day for 1 week. After acclimation, basal
running endurance was determined by placing each mouse on a
treadmill, gradually increasing the speed from 0 to 15 m/min, and
maintaining 15 m/min until the mouse was exhausted. The time and
distance run until exhaustion were recorded as the basal endurance
values (Week 0).
[0142] Mice then were treated once per day for 4 weeks with vehicle
or the PPAR.delta. agonist, GW1516 (5 mg/kg). Treatments were
administered orally. During the treatment period, mice were housed
in standard laboratory cages and received only the amount of
physical activity that could be had by normal movements about such
cage.
[0143] Animals were euthanized by carbon dioxide asphyxiation 72
hours after the final treatment. Gastrocnemius and quadriceps
muscles were isolated, frozen and stored at -80.degree. C. for
future analysis. Total RNA was prepared from quadriceps muscle
using TRIZOL.TM. reagent (Invitrogen, Calsbad, Calif., USA) in
conformance with manufacturer's instructions. Real time
quantitative PCR (QPCR) was used to determine expression levels of
uncoupling protein 3 (UCP3), muscle carnitine palmitoyl transferase
I (mCPT I) and pyruvate dehydrogenase kinase 4 (PDK4) using primers
known to those of ordinary skill in the art.
[0144] As shown in FIG. 1A, four weeks of GW1516 treatment induced
the expression of UCP3, mCPT I, and PDK4, in quadriceps muscle of
treated mice (compare V to GW). These changes in gene expression
were detected as early as 4 days after treatment and with drug
concentrations ranging from 2-5 mg/kg/day. Moreover, in the gene
expression studies, maximal effects of PPAR.delta. activation were
detected in pre-dominantly fast-twitch (quadricep and
gastrocnemius) but not slow-twitch (soleus) muscles.
[0145] Using primary muscle cells cultured from wild type and
PPAR.delta. null mice (Chawla et al., Proc. Natl. Acad. Sci. USA.
100(3): 1268-73, 2003; Man et al., J. Invest. Dermatol. 2007; Rando
and Blau, J. Cell. Biol. 125(6): 1275-87, 1994), it was confirmed
that the induction of oxidative genes by GW1516 is mediated via
activation of PPAR.delta. in skeletal muscles (FIGS. 1B-D).
Moreover, this is similar to the expression changes found in the
same gene set in muscles from mice expressing the constitutively
active VP16-PPAR.delta. transgene (Wang et al., PLoS Biol., 2:e294,
2004) (FIG. 1A, see TG). Collectively, these results indicate that
pharmacological activation of PPAR.delta. can initiate an oxidative
response in adult skeletal muscle.
[0146] Expression of biomarkers characteristic of an oxidative
phenotype in skeletal muscle, typically, has been correlated with
increased oxidative performance (e.g., increased running endurance)
of such skeletal muscle. This correlation was observed, for
instance, in the VP16-PPAR.delta. transgenic mouse (Wang et al.,
PLoS Biol., 2:e294, 2004). For this and other reasons, it was
expected that GW1516 treatment similarly would increase running
performance. Accordingly, to determine the functional effects of
ligand, age and weight matched cohorts of treated and control mice
were subjected to an endurance treadmill performance test before
(week 0) and after (week 5) treatment.
[0147] Following four weeks of treatment and housing in standard
laboratory cages without additional exercise, the running endurance
of GW1516-treated and control mice again was determined as
described above. Remarkably, and despite expectations for
improvement, GW1516-treated mice did not significantly differ from
controls in either the time spent or distance run on the treadmill
prior to exhaustion (FIG. 1E). Furthermore, long-term drug
treatment of up to 5 months also did not change running
endurance.
[0148] These results indicate that although in non-trained adult
muscle pharmacological activation of PPAR.delta. induces some
transcriptional changes, it fails to alter either fiber type
composition or endurance. In summary, pharmacologic activation of
the PPAR.delta. genetic program in adult C57B1/6J mice is
insufficient to promote a measurable enhancement of treadmill
endurance.
Example 2
Administration of PPAR.delta. Agonist Remodels Skeletal Muscle in
Exercised-Trained Subjects
[0149] Fiber type proportions in skeletal muscle are believed to be
determined by heredity and environmental factors, such as physical
activity level (Simoneau and Bouchard, FASEB J., 9(11):1091-1095,
1995; Larsson and Ansved, Muscle Nerve, 8(8):714-722, 1985).
Endurance exercise training is known to remodel the skeletal muscle
by increasing type I slow-twitch fibers, oxidative enzymes, and
mitochondrial density, which progressively alter performance
(Holloszy et al., J. Appl. Physiol. 56:831-8, 1984; Booth et al.,
Physiol Rev. 71:541-85, 1991; Schmitt et al., Physiol. Genomics.
15:148-57, 2003; Yoshioka et al., FASEB J. 17:1812-9, 2003; Mahoney
et al., Phys. Med. Rehabil. Clin. N. Am. 16:859-73, 2005; Mahoney
et al., FASEB J. 19:1498-500, 2005; Siu et al., J. Appl. Physiol.
97:277-85, 2004; Garnier et al., FASEB J. 19:43-52, 2005; Short et
al., J. Appl. Physiol. 99:95-102, 2005; Timmons et al., FASEB J.
19: 750-60, 2005). This example demonstrates that PPAR.delta.
agonist treatment influences skeletal muscle on a molecular
level.
[0150] To determine whether co-administration of GW1516 in the
context of endurance exercise can enhance changes in fiber type
composition and mitochondrial biogenesis, the effect of GW1516
treatment on muscle fiber-type composition was determined by
meta-chromatic staining of cryo-sections of gastrocnemius as
described by Wang et al. (PLoS Biol., 2:e294, 2004). Meta-chromatic
staining was used, following a routine myofibrillar ATPase
reaction, to demonstrate quantitative differences in phosphate
deposition among different skeletal muscle fiber types and,
thereby, differentiate skeletal muscle fiber types (Doriguzzi et
al., Histochem., 79(3):289-294, 1983; Ogilvie and Feeback, Stain
Technol., 65(5):231-241, 1990). In this assay, muscle fibers with
high ATPase activity (e.g., type I (slow oxidative) muscle fibers)
are darkly stained.
[0151] As shown in FIG. 2A, there was no significant difference in
the proportion of type I (slow, oxidative) muscle fibers in the
gastrocnemius muscles of vehicle- and GW1516-treated sedentary
mice. In contrast, hindlimb muscles of VP16-PPAR.delta. transgenic
mice exhibited an increased number of type I muscle fibers when
assayed by monochromatic staining. In trained mice, GW1516
increased the proportion of type I fibers (by 38%) compared to the
vehicle-treated sedentary mice (FIGS. 2A and 2B). Therefore,
administration of a PPAR.delta. agonist (e.g., GW1516) alone to
sedentary subjects does not significantly affect the number of type
I (slow-twitch, oxidative) muscle fibers in hindlimb muscles, but
can increase the number of type I muscle fibers in hindlimb muscles
of trained subjects.
[0152] In addition to its effects on the fiber type, exercise
training increased skeletal muscle mitochondrial biogenesis, which
can be measured as a function of mitochondrial DNA expression
levels using quantitative real time PCR (QPCR). Mitochondrial DNA
expression levels were determined in muscles of V, GW, Tr, and
GW+Tr subjects using quantitative real time PCR. As shown in FIG.
2C, similar to type I fiber changes, mitochondrial DNA expression
was not changed by drug alone but was increased by approximately
50% with the combination of exercise and GW1516 treatment (FIG.
2C). Such an increase is known to contribute to enhanced endurance
capacity (e.g., Holloszy, Med. Sci. Sports 7: 155-64, 1975).
[0153] Slow-twitch and fast-twitch muscle fiber types also can be
distinguished by myosin isoform expression (Gauthier and Lowey, J.
Cell Biol. 81:10-25, 1979; Fitzsimons and Hoh, Biochem. J.
193:229-33, 1981). Myosin isoform expression in skeletal muscle
adapts to various conditions, such as changes in muscle mechanics,
muscle innervation, or exercise paradigm (for review, see, e.g.,
Baldwin and Haddad, J. Appl. Physiol., 90(1):345-57, 2001; Baldwin
and Haddad, Am. J. Phys. Med. Rehabil., 81(11 Suppl):S40-51, 2002;
Parry, Exerc. Sport Sci. Rev., 29(4):175-179, 2001). The effect of
GW1516 administration on myosin heavy chain (MHC) expression (MHC
I, MHC IIa, MHC IIb) was determined by methods known to those of
ordinary skill in the art.
[0154] GW1516 treatment in sedentary mice increased the expression
of MHC I (a marker of slow-twitch, oxidative muscle fibers) and
decreased the expression of MHC IIb (a marker of fast-twitch,
glycolytic muscle fibers) as compared to vehicle-treated, control
mice. In comparison, GW1516 treatment did not alter the expression
of MHC IIa (a marker of fast-twitch oxidative/glycolytic muscle
fibers) in sedentary mice. Therefore, at least at the
transcriptional level, the PPAR.delta. agonist was capable of
inducing some proteins characteristic of a slow-twitch muscle fiber
phenotype.
[0155] In summary, expression of constitutively active PPAR.delta.
in the skeletal muscles of VP16-PPAR.delta. transgenic mice
resulted in a "long-distance running phenotype" with "profound and
coordinated increases in oxidative enzymes, mitochondrial
biogenesis and production of specialized type I fiber contractile
proteins--the three hallmarks of muscle fiber type switching" (Wang
et al., PLoS Biol., 2:e294, 2004). In contrast, pharmacological
activation of PPAR.delta. in normal subjects only partially
recapitulated VP16-PPAR.delta. transgenesis by regulating some
metabolic genes. Markedly, administration of a PPAR.delta. agonist
to sedentary subjects did not lead to a change in fiber type
specification (as measured by monochromatic staining) or enhance
exercise endurance. Transgenic over-expression of activated
PPAR.delta. at birth pre-programs the nascent myofibers to
trans-differentiate into slow-twitch fibers, thus imparting a high
basal endurance capacity to adult transgenic mice. In contrast,
since fiber type specification is completed prior to exposure of
adults to PPAR.delta. agonist, the potential plasticity of muscle
to drug treatment alone is virtually non-existent.
[0156] This example illustrates that the genetic or pharmacologic
activation of the PPAR.delta. regulatory program in skeletal
muscles of adult, sedentary subjects does not have the same
outcome. The ability to genetically manipulate skeletal muscle
specification by activation of the PPAR.delta. receptor in a
transgenic mouse from early development in the absence of exercise
is not necessarily predictive of the result of pharmacologically
activating the PPAR.delta. program in the sedentary, normal adult.
The cellular "template" for PPAR.delta. effects on skeletal muscle
is very different in a normal subject as compared to a genetically
engineered transgenic subject. For example, in a normal adult,
muscle fiber specification of individual muscle groups is already
determined and the connections between muscle fibers and spinal
motor neurons are established prior to pharmacological activation
of the PPAR.delta.-regulated program. In the transgenic mouse, the
constitutively active PPAR.delta. transgene is active all the while
muscle fiber specification is being determined and connections
between muscle fibers and motor neurons are being made. In
addition, the effects of activation of endogenous PPAR.delta.
receptor by a single daily dose of a PPAR.delta. agonist, which is
expect to have a transient peak exposure followed by clearance,
likely are much different from the effects of the constitutive
activation of a VP16-PPAR.delta. transgene.
Example 3
The Combination of PPAR.delta. Agonist Treatment and Exercise
Training Significantly Affected Fatty Acid Metabolism and Markers
of Fatty Acid Oxidation
[0157] In addition to affecting the contractile apparatus of
skeletal muscle, exercise training also increases skeletal muscle
mitochondrial density (e.g., Freyssenet et al., Arch. Physiol.
Biochem., 104(2):129-141, 1996). This Example illustrates that
PPAR.delta. agonist treatment (e.g., GW1516) in exercise-trained
subjects affected fatty acid metabolism in exercised muscle.
[0158] The effects of GW1516 treatment and exercise, alone or in
combination, on components of the oxidative metabolism of fatty
acids were determined by measuring gene expression levels of
selective biomarkers for fatty acid .beta.-oxidation (FAO). Male
C57B/6J mice (8-10 wks old) were randomly divided into four groups
(nine per group): (i) vehicle-treated and sedentary (V), (ii)
GW1516-treated and sedentary (GW), (iii) vehicle-treated and
exercise trained (Tr) and (iv) GW1516-treated and exercise trained
(GW+Tr). Mice in all groups were acclimated to moderate treadmill
running and basal running endurance was determined as described in
Example 1. Thereafter, mice in the exercise-trained groups received
four weeks (5 days/week) of exercise training on a treadmill
inclined at 5 degrees. Intensity and time of training were
gradually increased. At the end of four weeks, all exercise-trained
mice were running for 50 min/day at 18 m/min. Vehicle or GW1516 was
administered to the respective exercise-treated or sedentary groups
as described in Example 1. Unless otherwise noted, V, GW, Tr and
GW+Tr subjects described in this and the examples below were
similarly treated. At the end of the drug treatment and/or training
protocol (Week 5) 6 mice per group were subjected to the running
test. These interventions do not affect body weight and food intake
in mice. RNA was prepared real time quantitative PCR performed as
described in Example 1.
[0159] Confirming the results obtained in Example 1, UCP3, mCPT I,
and PDK4 were upregulated by GW1516 but showed no further induction
with exercise (see FIGS. 1A and 3A). Unexpectedly, a second set of
genes were identified that showed no response to exercise or GW1516
alone but were robustly induced by the combination. This intriguing
response profile includes a series of genes involved in the
regulation of fatty acid storage [such as steroyl-CoA-desaturase
(SCD1), fatty acyl coenzyme A synthase (FAS) and serum response
element binding protein 1c (SREBP1c)] and fatty acid uptake [such
as the fatty acid transporter (FAT/CD36) and lipoprotein lipase
(LPL)] adding a new set of target genes to exercise and drug
treated mice (FIGS. 3B, 3C and 6A-C).
[0160] In addition to gene expression, protein expression was
determined for selective oxidative biomarkers including myoglobin,
UCP3, cytochrome c (CYCS) and SCD1, using Western blotting. Protein
homogenates were prepared from quadriceps muscle, separated by SDS
polyacrylamide gel electrophoresis, transferred to blotting
membrane and probed with antibodies specific for myoglobin (Dako),
UCP3 (Affinity Bioreagents), cytochrome c (Santacruz) SCD1
(Santacruz), and, as a loading control, tubulin (Sigma). A robust
up regulation of myoglobin, UCP3, cytochrome c, and SCD1 protein
expression was observed with combined exercise and GW1516 treatment
in comparison to treatment with the PPAR.delta. agonist or exercise
alone (FIG. 3D).
[0161] Altered triglycerides can be used to access changes in
muscle oxidative capacity. Muscle triglyceride (mTG) content was
measured as previously described (Wang et al., PLoS Biol., 2:e294,
2004) using a kit from Thermo Electron Corporation. As shown in
FIG. 4, mTG content was comparable between vehicle and
GW1516-treated sedentary mice and was substantially increased in
muscle of mice receiving only exercise training. In contrast,
dramatic increase in triglycerides in exercised muscle was
completely reversed in GW1516-treated exercise trained mice,
indicating increased fat utilization (FIG. 4).
[0162] Gene and/or protein expression that is induced by a
combination of exercise and drug treatment (e.g., PPAR.delta.
agonist administration) but not by either input alone is believed
to be a new discovery. This type of response can be used to further
characterize the intersection of pharmacologic and physiologic
genetic networks. For example, one or more genes and/or proteins
uniquely regulated by one or more drugs (e.g., PPAR.delta.
agonists) and exercise can be used as markers, for instance, of
illicitly boosting performance in professional and/or amateur
athletes.
Example 4
Administration of PPAR.delta. Agonist Enhances the Physical
Performance of Exercise-Trained Subjects
[0163] As described in Example 1, although GW1516 treatment induces
wide-spread genomic changes associated with oxidative metabolism,
nonetheless alone it failed to increase running endurance. This
finding was unexpected because it was known that constitutive
activation of the PPAR.delta. gene network (in the VP16-PPAR.delta.
transgenic mouse) lead to a distance-running phenotype (familiarly,
a "marathon mouse"). On the other hand, as surprisingly shown in
Example 3, PPAR.delta. agonist (e.g., GW1516) treatment in
conjunction with exercise produced an enriched remodeling program
that included a series of transcriptional and post-translational
adaptations in the skeletal muscle. This indicates that exercise
training serves as a trigger to unmask a set of PPAR.delta. target
genes. This Example provides methods used to demonstrate that
administration of a PPAR.delta. agonist (e.g., GW1516) surprisingly
improves physical performance in exercised (trained) subjects.
[0164] Male C57B/6J mice (8-10 wks old) were randomly divided into
four groups (nine per group): (i) vehicle-treated and sedentary
(V), (ii) GW1516-treated and sedentary (GW), (iii) vehicle-treated
and exercise trained (Tr) and (iv) GW1516-treated and exercise
trained (GW+Tr), acclimated to moderate treadmill running as
described in Example 1, and exercise-trained as described in
Example 3. At the end of the drug treatment and/or training
protocol (Week 5) 6 mice per group were subjected to the running
test.
[0165] At the end of the drug treatment and/or training protocol
(Week 5), running endurance of six mice per group was determined in
the same manner as was basal running endurance. No follow-up
endurance tests were performed on three mice in each group to
confirm that changes observed in the skeletal muscle were not due
to the acute run, but were related to the exercise training.
[0166] As shown in FIGS. 5A and 5B, the same dose and duration of
GW1516 treatment that failed to alter running endurance in
sedentary mice, when paired with 4 weeks of exercise training,
increases running time by 68% and running distance by 70% over
vehicle-treated trained mice (FIGS. 5A and 5B, compare Week 5).
Comparison of running time and distance before (week 0) and after
(week 5) exercise and drug treatment revealed a 100% increment in
endurance capacity for individual mice, underscoring the robustness
of the combination paradigm (FIGS. 5A and 5B). In contrast, the
same exercise protocol without concurrent GW1516 treatment did not
significantly increase running endurance in C57B1/6J mice.
[0167] Hematoxylin and eosin (H&E) staining of white adipose
tissue paraffin sections was performed as previously described
(Wang et al., PLoS Biol., 2:e294, 2004; Wang et al., Cell, 113:
159-70, 2003). As shown in FIG. 5C, GW1516 treatment in combination
with exercise produced a significant (32%) reduction in the
epididymal fat to body weight ratio, which was further evident in
the decreased cross-sectional area of the adipocytes in the same
group (FIG. 5D). Therefore, the combined effects of GW1516 and
exercise are not restricted to muscle.
[0168] Using the methods described in Example 2, it was also
demonstrated that the combination of GW1516 treatment and exercise
training significantly increased the number of type I muscle fibers
in exercised muscle. However, combining GW1516 treatment with
exercise did not induce additional changes in MHC I and MHC IIb
expression. Therefore, although orally administered PPAR.delta.
agonist (GW1516) alone is capable of inducing the expression of at
least some of the contractile proteins in the PPAR.delta.-regulated
gene network (see Example 5) the transcriptional effect observed
was not sufficient to induce a post-transcriptional change in
fiber-type composition as was observed by meta-chromatic staining
in GW1516-treated, exercised mice.
[0169] This Example illustrates that PPAR.delta. agonist (e.g.,
GW1516) treatment unexpectedly augments the performance of aerobic
exercise (e.g., running distance and endurance) in an exercised
subject. Endurance exercise is known to channel extra-muscular fat
to muscle triglyceride stores by inducing adipose tissue lipolysis
to meet increased oxidative demands (Despres et al., Metabolism,
33:235-9, 1984; Mauriege et al., Am. J. Physiol., 273:E497-506,
1997; Mader et al., Int. J. SportsMed., 22:344-9, 2001; Schmitt et
al., Physiol. Genomics, 15:148-57, 2003; Schrauwen-Hinderling et
al., J. Clin. Endocrinol. Metab., 88:1610-6, 2003). In addition,
the induction of FAO components and selective up-regulation of
fatty acid storage and up-take components in GW1516-treated,
exercised mice described in Example 3 indicate enhanced
mobilization of fat as fuel in skeletal muscle. Therefore, combined
exercise and GW1516 treatment dramatically increases muscle
oxidative capacity in subjects, for example by increasing local
fatty acid synthesis and/or mobilizing fatty acid stores from
adipose tissue.
[0170] This is the first demonstration of how an orally active
PPAR.delta. agonist and exercise can co-operatively re-program the
muscle genome and raise endurance limits.
Example 5
The Combination of PPAR.delta. Agonist Treatment and Exercise
Training Produced a Unique Gene Expression Signature in Exercised
Muscle
[0171] A comprehensive study of the skeletal muscle transcriptional
program in V, GW, Tr and Tr+GW mice was conducted using microarray
analysis. Affymetrix.TM. high-density oligonucleotide array mouse
genome 430A 2.0 chips were used. Preparation of in vitro
transcription products, oligonucleotide array hybridization, and
scanning were performed in conformance with Affymetrix.TM.-provided
protocols. To minimize discrepancies due to variables, the raw
expression data were scaled by using Affymetrix.TM. MICROARRAY
SUITE.TM. 5.0 software, and pairwise comparisons were performed.
The trimmed mean signal of all probe sets was adjusted to a
user-specified target signal value (200) for each array for global
scaling. No specific exclusion criteria were applied. Additional
analyses were performed using the freeware program BULLFROG 7
(available on the internet Barlow-LockhartBrainMapNIMHGrant.org)
and the Java-based statistical tool VAMPIRE (Hsiao et al.,
Bioinformatics, 20:3108-3127, 2004).
[0172] Genome-wide analysis of the quadriceps muscle revealed that
GW1516 treatment, exercise, and the combination regulated 96, 113
and 130 genes, respectively (FIG. 6). Approximately 50% of the
target genes regulated by GW1516 or exercise alone were the same,
demonstrating that PPAR.delta. activation of the gene network
partially mimics exercise effects on the same network.
[0173] The 130 genes regulated by the combination of GW1516
treatment and exercise training and a classification of each such
gene are shown in Table 1. The 130 regulated genes included 30 fat
metabolism genes, 5 oxygen carriers, 5 mitochondrial genes, 3
carbohydrate metabolism genes, 15 signal transduction genes, 16
transcription genes, 10 transport genes, 3 steroid biogenesis
genes, 5 heat shock genes, 2 angiogenesis genes, 5 proliferation
and apoptosis genes, 2 cytokines, and 29 others. The majority of
the genes in the exercise-trained/GW1516-treated (GW+Tr) gene
signature shown in Table 1 were induced (109/130). The 109
upregulated genes are shown in non-bold font in Table 1 (final
column>1). Down-regulated genes are shown in bold italics in
Table 1 (final column<1).
TABLE-US-00002 TABLE 1 Genes regulated by GW1516 treatment and
exercise training FEATURE LOCUS DESCRIPTION GW + Tr ANGIOGENESIS
1417130_s_at Angptl4 angiopoietin-like 4 5.495 CARBOHYDRATE
METABOLISM 1449088_at Fbp2 fructose bisphosphatase 2 2.808
1423439_at Pck1 phosphoenolpyruvate carboxykinase 1, cytosolic
3.518 1434499_a_at Ldhb lactate dehydrogenase B 2.541 PROLIFERATION
& APOPTOSIS 1425621_at Trim35 tripartite motif-containing 35
1.856 1448272_at Btg2 B-cell translocation gene 2,
anti-proliferative 1.601 1452260_at Cidec cell death-inducing
DFFA-like effector c 4.771 1417956_at Cidea cell death-inducing DNA
fragmentation factor, alpha 49.625 subunit-like effector A
CYTOKINES 1426278_at Ifi27 interferon, alpha-inducible protein 27
1.714 1421239_at Il6st interleukin 6 signal transducer 1.972 FAT
METABOLISM 1448318_at Adfp adipose differentiation related protein
2.009 1424729_at BC054059 cDNA sequence BC054059 5.08 1424937_at
2310076L09Rik RIKEN cDNA 2310076L09 gene 1.868 1450010_at Hsd17b12
hydroxysteroid (17-beta) dehydrogenase 12 2.376 1415965_at Scd1
stearoyl-Coenzyme A desaturase 1 6.494 1415822_at Scd2
stearoyl-Coenzyme A desaturase 2 1.849 1423828_at Fasn fatly acid
synthase 6.323 1455061_a_at Acaa2 acetyl-Coenzyme A acyltransferase
2 (mitochondrial 3- 1.926 oxoacyl-Coenzyme A thiolase) 1448987_at
Acadl acetyl-Coenzyme A dehydrogenase, long-chain 2.549 1422651_at
Adipoq adiponectin, C1Q and collagen domain containing 3.082
1422820_at Lipe lipase, hormone sensitive 3.032 1449964_a_at Mlycd
malonyl-CoA decarboxylase 1.781 1426785_s_at Mgll monoglyceride
lipase 1.907 1420658_at Ucp3 uncoupling protein 3 (mitochondrial,
proton carrier) 2.943 1425326_at Acly ATP citrate lyase 2.606
1460409_at Cpt1a carnitine palmitoyltransferase 1a, liver 2.753
1422677_at Dgat2 diacylglycerol O-acyltransferase 2 2.784
1425834_a_at Gpam glycerol-3-phosphate acyltransferase,
mitochondrial 2.207 1417273_at Pdk4 pyruvate dehydrogenase kinase,
isoenzyme 4 2.27 1449182_at Retn resistin 4.114 1435630_s_at Acat2
acetyl-Coenzyme A acetyltransferase 2 1.625 1425829_a_at Abcb1a
ATP-binding cassette, sub-family B (MDR/TAP), member 10.322 1A
1423166_at Cd36 CD36 antigen 1.584 1422811_at Slc27a1 solute
carrier family 27 (fatty acid transporter), member 1 3.58
1416023_at Fabp3 fatty acid binding protein 3, muscle and heart
1.833 1424155_at Fabp4 fatty acid binding protein 4, adipocyte
2.189 1431056_a_at Lpl lipoprotein lipase 1.659 1422432_at Dbi
diazepam binding inhibitor 1.936 1422811_at Slc27a1 solute carrier
family 27 (fatty acid transporter), 1 3.58 HEAT SHOCK RESPONSE
1448881_at Hp haptoglobin 1.679 1427126_at Hspa1b heat shock
protein 1B 8.845 1438902_a_at Hsp90aa1 heat shock protein 90 kDa
alpha (cytosolic), class A 1.513 member 1 1431274_a_at Hspa9a heat
shock protein 9A 1.61 1416755_at Dnajb1 DnaJ (Hsp40) homolog,
subfamily B, member 1 3.59 MISCELLANEOUS 1460256_at Car3 carbonic
anhydrase 3 2.339 1415841_at Dync1i2 dynein cytoplasmic 1
intermediate chain 2 1.705 1432344_a_at Aplp2 amyloid beta (A4)
precursor-like protein 2 1.937 1416429_a_at Cat catalase 1.82
1418306_at Crybb1 crystallin, beta B1 2.457 1448842_at Cdo1
cysteine dioxygenase 1, cytosolic 3.266 1453527_a_at Neurl
neuralized-like homolog (Drosophila) 1.941 1451603_at Rtbdn
retbindin 2.32 1453724_a_at Serpinf1 serine (or cysteine) peptidase
inhibitor, clade F, member 1 7.765 1427285_s_at Surf4 surfeit gene
4 2.091 1424737_at Thrsp thyroid hormone responsive SPOT14 homolog
(Rattus) 2.685 1431609_a_at Acp5 acid phosphatase 5, tartrate
resistant 3.91 1448538_a_at D4Wsu53e DNA segment, Chr 4, Wayne
State University 53, 1.586 expressed 1425552_at Hip1r huntingtin
interacting protein 1 related 1.75 1429360_at Klf3 Kruppel-like
factor 3 (basic) 1.901 1449413_at Mpv17l Mpv17 transgene, kidney
disease mutant-like 1.988 1451667_at C530043G21Rik RIKEN cDNA
C530043G21 gene 1.5 1425865_a_at Lig3 ligase III, DNA,
ATP-dependent 2.693 1415994_at Cyp2e1 cytochrome P450, family 2,
subfamily e, polypeptide 1 2.941 1417867_at Cfd complement factor D
(adipsin) 2.828 1451015_at Tkt transketolase 2.256 1432344_a_at
Aplp2 amyloid beta (A4) precursor-like protein 2 1.937 1419487_at
Mybph Myosin binding protein H 1.578 MITOCHONDRIAL PROTEINS
1415897_a_at Mgst1 microsomal glutathione S-transferase 1 1.916
1423109_s_at Slc25a20 solute carrier family 25 (mitochondrial 1.865
carnitine/acylcarnitine translocase), member 20 OXYGEN CARRIERS
1448348_at Gpiap1 GPI-anchored membrane protein 1 1.83 1451203_at
Mb myoglobin 1.578 1428361_x_at Hba-a1 hemoglobin alpha, adult
chain 1 1.632 1417184_s_at Hbb-b2|Hbb-y hemoglobin, beta adult
minor chain|hemoglobin Y, beta- 1.626 like embryonic chain SIGNAL
TRANSDUCTION 1455918_at Adrb3 adrenergic receptor, beta 3 3.83
1452097_a_at Dusp7 dual specificity phosphatase 7 1.661 1419191_at
Hipk3 homeodomain interacting protein kinase 3 1.694 1448152_at
Igf2 insulin-like growth factor 2 1.635 1422313_a_at Igfbp5
insulin-like growth factor binding protein 5 1.772 1428265_at
Ppp2r1b protein phosphatase 2 (formerly 2A), regulatory subunit A
2.509 (PR 65), beta isoform 1449342_at Ptplb protein tyrosine
phosphatase-like (proline instead of 2.38 catalytic arginine),
member b 1422119_at Rab5b RAB5B, member RAS oncogene family 1.603
1425444_a_at Tgfbr2 transforming growth factor, beta receptor II
2.13 1431164_at Rragd Ras-related GTP binding D 2.101 1420816_at
Ywhag 3-monooxygenase/tryptophan 5-monooxygenase activation 1.87
protein, gamma polypeptide STEROID BIOGENESIS 1418601_at Aldh1a7
aldehyde dehydrogenase family 1, subfamily A7 3.862 1426225_at Rbp4
retinol binding protein 4, plasma 2.065 TRANSCRIPTION 1417794_at
Zfp261 zinc finger protein 261 1.847 1424731_at Nle1 notchless
homolog 1 (Drosophila) 1.831 1454791_a_at Rbbp4 retinoblastoma
binding protein 4 2.865 1460281_at Asb15 ankyrin repeat and SOCS
box-containing protein 15 1.78 1449363_at Atf3 activating
transcription factor 3 1.802 1418982_at Cebpa CCAAT/enhancer
binding protein (C/EBP), alpha 2.168 1417065_at Egr1 early growth
response 1 2.577 1415899_at Junb Jun-B oncogene 1.792 1421554_at
Lmx1a LIM homeobox transcription factor 1 alpha 4.106 1416959_at
Nr1d2 nuclear receptor subfamily 1, group D, member 2(Reverb-b)
1.794 1450749_a_at Nr4a2 nuclear receptor subfamily 4, group A,
member 2 (NURR1) 1.776 1460215_at Rpo1-4 RNA polymerase 1-4 2.498
1420892_at Wnt7b wingless-related MMTV integration site 7B 4.449
1423100_at Fos FBJ osteosarcoma oncogene 3.9 TRANSPORT PROTEINS
1425546_a_at Trf transferrin 1.907 1423743_at Arcn1 archain 1 1.617
1451771_at Tpcn1 two pore channel 1 2.842 1416629_at Slc1a5 solute
carrier family 1 (neutral amino acid transporter), 1.939 member 5
1420295_x_at Clcn5 chloride channel 5 2.333 1417839_at Cldn5
claudin 5 1.545 1434617_x_at 1810073N04Rik RIKEN cDNA 1810073N04
gene 2.326 Data is average of N = 3 samples in each group (p <
0.05).
[0174] Surprisingly, the combination of GW1516 treatment and
exercise established a unique gene expression pattern that was
neither an amalgamation nor a complete overlap of the two
interventions (FIG. 6). This unique signature included 48 new
target genes (Table 2) not regulated by GW1516 and exercise alone
and excluded 74 genes regulated by GW1516 or exercise alone (a
selected few of which are shown in Table 3). This signature for the
combination of GW1516 treatment and exercise (Table 2) was highly
enriched in genes encoding regulatory enzymes for energy
homeostasis, angiogenesis, oxygen transport, signal transduction,
transcription and substrate transport, which are processes that are
involved in endurance adaptation. Particularly, a predominance of
genes involved in oxidative metabolism, is selectively up-regulated
by combined exercise and drug treatment (see unbolded genes in
Tables 1 and 2). In addition, several stress-related genes
activated by either intervention, including heat shock proteins,
metallothioneins and other stress biomarkers (Table 3) are not
changed by the combination possibly reflecting a potential
lessening of exercise-based damage.
TABLE-US-00003 TABLE 2 Gene targets unique to combined GW1516
treatment and exercise training. DESCRIPTION LOCUS GW + Tr
ANGIOGENESIS CARBOHYDRATE METABOLISM phosphoenolpyruvate
carboxykinase 1, cytosolic Pck1 3.518 CYTOKINES interferon,
alpha-inducible protein 27 Ifi27 1.714 FAT METABOLISM adipose
differentiation related protein Adrp 2.009 stearoyl-Coenzyme A
desaturase 2 Scd2 1.849 acetyl-Coenzyme A acetyltransferase 2 Acat2
1.625 ATP citrate lyase Acly 2.606 adiponectin, C1Q and collagen
domain containing Adipoq 3.082 diacylglycerol O-acyltransferase 2
Dgat2 2.784 lipase, hormone sensitive Lipe 3.032 monoglyceride
lipase Mgll 1.907 resistin Retn 4.114 CD36 antigen Cd36 1.584 fatty
acid binding protein 4, adipocyte Fabp4 2.189 lipoprotein lipase
Lpl 1.659 HEAT SHOCK RESPONSE haptoglobin Hp 1.679 MITOCHONDRIAL
PROTEINS microsomal glutathione S-transferase 1 Mgst1 1.916 OTHERS
carbonic anhydrase 3 Car3 2.339 cysteine dioxygenase 1, cytosolic
Cdo1 3.266 DNA segment, Chr 4, Wayne State University 53, expressed
D4Wsu53e 1.586 dynein cytoplasmic 1 intermediate chain 2 Dync1i2
1.705 Kruppel-like factor 3 (basic) Klf3 1.901 thyroid hormone
responsive SPOT14 homolog (Rattus) Thrsp 2.685 cytochrome P450,
family 2, subfamily e, polypeptide 1 Cyp2e1 2.941 complement factor
D (adipsin) Cfd 2.828 transketolase Tkt 2.256 OXYGEN CARRIERS
GPI-anchored membrane protein 1 Gpiap1 1.83 PROLIFERATION &
APOPTOSIS cell death-inducing DFFA-like effector c Cidec 4.771
SIGNAL TRANSDUCTION dual specificity phosphatase 7 Dusp7 1.661
homeodomain interacting protein kinase 3 Hipk3 1.694 insulin-like
growth factor binding protein 5 Igfbp5 1.772 protein phosphatase 2
(formerly 2A), regulatory subunit A (PR 65), beta Ppp2r1b 2.509
isoform protein tyrosine phosphatase-like (proline instead of
catalytic arginine), Ptplb 2.38 member b STEROID BIOGENESIS retinol
binding protein 4, plasma Rbp4 2.065 TRANSCRIPTION CCAAT/enhancer
binding protein (C/EBP), alpha Cebpa 2.168 nuclear receptor
subfamily 1, group D, member 2(Reverb-b) Nr1d2 1.794 TRANSPORT
transferrin Trf 1.907 archain 1 Arcn1 1.617 solute carrier family 1
(neutral amino acid transporter), member 5 Slc1a5 1.939 RIKEN cDNA
1810073N04 gene 1810073N04Rik 2.326 Down-regulated genes are in
bold italics. (N = 3, each pooled from 3 mice, p < 0.05).
TABLE-US-00004 TABLE 3 Gene targets regulated by GW1516 treatment
or exercise training alone. FEATURE LOCUS DESCRIPTION GW Tr GW + Tr
Hspb1 heat shock protein 1 1.815 1.965 -- 1451284_at Hspb7 heat
shock protein family, 7 (cardiovascular) 3.414 1.753 --
1422943_a_at Dnaja1 DnaJ (Hsp40) homolog, subfamily A, 1 -- 1.545
-- 1421290_at Hsp110 heat shock protein 110 -- 1.587 -- 1416288_at
Serpinh1 serine (or cysteine) peptidase inhibitor, H, 1 -- 2.198 --
1423566_a_at Dnaja4 DnaJ (Hsp40) homolog, subfamily A, 4 1.756
1.545 -- 1417872_at Mt1 metallothionein 1 2.364 -- -- 1424596_s_at
Mt2 metallothionein 2 2.151 -- -- 1416157_at Cryab crystallin,
alpha B 1.561 1.52 -- 1423139_at Crygf crystallin, gamma F 1.801
3.56 -- 1448830_at Smad3 MAD homolog 3 (Drosophila) 1.841 1.886 --
1450637_a_at Ankrd1 ankyrin repeat domain 1 (cardiac muscle) 4.235
-- -- 1416029_at Tnfrsf12a TNF receptor superfamily, 12a 1.759
1.782 -- 1426464_at Jun Jun oncogene -- 1.521 -- Data is average of
N = 3 samples in each group (p < 0.05)
[0175] Thirty-two percent of the GW+Tr-regulated genes encode
enzymes of metabolic pathways such as fatty acid
biosynthesis/storage (e.g., FAS, SCD 1 & 2), uptake [e.g.,
FAT/CD36, fatty acid binding proteins (FABP) and LPL] and oxidation
[e.g., adiponectin, hormone sensitive lipase (HSL), PDK4, UCP3];
and carbohydrate metabolism [e.g., fructose bisphosphate 2 (FBP2),
phosphoenolpyruvate carboxykinase 1 (PEPCK1), lactate dehydrogenase
B], which along with oxygen transporters and mitochondrial proteins
form the largest class of genes directly linked to muscle
performance (Ikeda et al., Biochem. Biophys. Res. Commun.
296:395-400, 2002; Achten and Jeukendrup, Nutrition. 20:716-27,
2004; Hittel et al., J. Appl. Physiol. 98: 168-79, 2005; Civitarese
et al., CellMetab. 4:75-87, 2006; Nadeau et al., FASEB J 17:1812-9,
2006; Kiens, Physiol. Rev. 86:205-43, 2006; Yamauchi et al., Nat.
Med. 8:1288-95, 2006). Unexpectedly, established PPAR.alpha. target
genes fatty acyl-CoA oxidase and medium chain acyl-CoA
dehydrogenase (MCAD) were not represented in the signature. All but
four of these metabolic genes were induced, which indicated a
general increase in oxidative capacity of skeletal muscle in
exercise-trained subjects that received GW1516 treatment.
[0176] Other genes regulated in quadriceps muscle by the
combination of exercise and GW1516 treatment encoded proteins
involved in pathways such as angiogenesis (e.g., angiopoietin-like
4 protein/also a known regulator of lipid metabolism), (e.g.,
adrenergic receptor .beta.3, insulin-like growth factor,
insulin-like growth factor binding protein 5), transcription (e.g.,
C/EBP .alpha., Reverb .beta., NURR1) and substrate transport (e.g.,
transferrin, chloride channel 5) (Nagase et al., J. Clin. Invest.
97:2898-904, 1996; Singleton and Feldman, Neurobiol. Dis. 8:541-54,
2001; Adams, J. Appl. Physiol. 93:1159-67, 2002; Centrella et al.,
Gene. 342: 13-24, 2004; Lundby et al., Eur. J. Appl. Physiol. 96:
363-9, 2005; Mahoney et al., FASEB J. 19:1498-500, 2005; Mahoney et
al., Phys. Med. Rehabil. Clin. N. Am. 16: 859-73, 2005;
Ramakrishnan et al., J. Biol. Chem. 280:8651-9, 2005). Without
wishing to be bound to a particular theory, such other genes are
likely involved, at least in part, in muscle remodeling and
increased endurance observed in GW1516-treated, exercise-trained
subjects.
[0177] Interestingly, comparative expression analysis of the 48
gene subset of the endurance signature (Table 2), but not of either
intervention alone, revealed a striking similarity to `untrained`
VP16-PPAR.delta. transgenic mice. This observation confirms the
primary dependence of the 48 genes on PPAR.delta. and indicates
that exercise-generated signals may function to synergize
PPAR.delta. transcriptional activity to levels comparable to
transgenic over-expression. Therefore, exercise cues along with
PPAR.delta. agonist may function to hyper-activate receptor
transcriptional activity to re-program of adult muscle.
[0178] Genes and/or proteins uniquely affected (e.g., up-regulated
or down-regulated or not substantially regulated) by exercise in
the presence of one or more pharmaceutical agents (e.g.,
PPAR.delta. agonists) can be used as markers, for instance, of
"drug doping" in exercise-trained subjects (e.g., athletes). It is
expected that the unique set of 48 genes regulated by GW+Tr, but
not GW1516 treatment or exercise training alone, can be used to
identify exercised subjects who have received a variety
performance-enhancing drugs.
Example 6
PPAR.delta. Directly Interacts with Exercise-Activated Kinases,
p44/42 MAPK and AMPK
[0179] Exercise training is known to activate kinases, such as
p44/42 MAPK and AMPK, which regulate gene expression in skeletal
muscle (Chen et al., Diabetes, 52:2205-12, 2003; Goodyear et al.,
Am. J. Physiol., 271:E403-8, 1996). AMPK affects skeletal muscle
gene expression and oxidative metabolism (Chen et al., Diabetes.
52: 2205-12, 2003, Reznick et al., J. Physiol. 574: 33-9, 2006).
The interaction between exercise-regulated kinases and PPAR.delta.
signaling is described in this Example.
[0180] The levels of phospho-p44/42 MAPK and phospho-AMPK
.alpha.subunit and total AMPK were determined in protein
homogenates of quadriceps muscle by Western blot. Antibodies
specific for phospho-p44/42 MAPK, phospho- and total-AMPK .alpha.1
antibodies were obtained from Cell Signaling. The phospho-specific
AMPK .alpha.c1 antibody recognizes the key activating threonine in
the activation loop.
[0181] Active forms of both kinases (phospho-p44/42 MAPK and
phospho-AMPK .alpha.subunit) were expressed at higher levels in the
quadriceps muscles of exercised mice relative to the sedentary
controls (FIG. 7A). Previous reports claim that PPAR.delta. is not
required for activation of AMPK by GW1516 in cultured cells (Kramer
et al, Diabetes. 54(4):1157-63, 2005 and Kramer et al., J. Biol.
Chem. 282(27):19313-2, 2007). In contrast, it was observed that
GW1516 failed to activate p44/42 or AMPK in either sedentary or
trained muscles, which indicated that PPAR.delta.-regulated effects
are downstream to the exercise-induced signals that activate these
kinases. Furthermore, AMPK appears to be constitutively active in
muscles of VP16-PPAR.delta. transgenic mice in absence of exercise
or drug (FIG. 7B). These results indicate that synergy is AMPK and
PPAR.delta. co-dependent.
[0182] If synergy is AMPK and PPAR.delta. co-dependent, selective
co-activation of AMPK and PPAR.delta. would induce gene expression
changes that mimic those triggered by combined exercise and
PPAR.delta. as well as VP16-PPAR.delta. over-expression. To
demonstrate this, transcriptional changes induced in skeletal
muscle by combined exercise and GW1516 treatment (as described in
Example 5) were compared to that of combined AMPK activator (the
cell permeable AMP analog AICAR; 250 mg/kg/day, i.p.) and GW1516 (5
mg/kg/day, oral gavage) treatment for 6 days. Genome analysis was
performed using the methods described in Example 5.
[0183] Simultaneous GW1516 and AICAR treatment for 6 days created a
unique gene expression signature in the quadriceps of untrained
C57B1/6J mice (FIG. 8A, which includes target genes associated with
translation, protein processing, amino acid metabolism, fat
metabolism, oxygen carriers, carbohydrate metabolism, signal
transduction, transcription, transport, steroid biogenesis, heat
shock response, angiogenesis, proliferation and apoptosis,
cytokines, contractile proteins, stress, and others) that shares
40% of the genes with that of combined GW1516 treatment and
exercise (FIG. 8B). Classification of the 52 genes common to the
two signatures (combined PPAR.delta. activation and exercise or
PPAR.delta. and AMPK co-activation) (listed in Table 4) revealed
that the majority of the targets were linked to oxidative
metabolism.
TABLE-US-00005 TABLE 4 Targets common to exercise-PPAR.delta. and
AMPK-PPAR.delta. gene signatures. DESCRIPTION LOCUS Tr + GW AI + GW
ANGIOGENESIS angiopoietin-like 4 Angptl4 5.495 2.917 APOPTOSIS cell
death-inducing DFFA-like effector c Cidec 4.771 1.838 cell
death-inducing DNA fragmentation factor, alpha Cidea 49.625 1.842
subunit-like effector A CARBOHYDRATE METABOLISM lactate
dehydrogenase B Ldhb 2.541 1.917 fructose bisphosphatase 2 Fbp2
2.808 2.478 FAT METABOLISM stearoyl-Coenzyme A desaturase 1 Scd1
6.494 1.78 fatty acid binding protein 3, muscle and heart Fabp3
1.833 1.5 pyruvate dehydrogenase kinase, isoenzyme 4 Pdk4 2.27
2.486 uncoupling protein 3 (mitochondrial, proton carrier) Ucp3
2.943 2.792 adiponectin, C1Q and collagen domain containin Adipoq
3.082 1.56 diacylglycerol O-acyltransferase 2 Dgat2 2.784 2.14
solute carrier family 27 (fatty acid transporter), member 1 Slc27a1
3.58 2.195 lipase, hormone sensitive Lipe 3.032 1.746 solute
carrier family 25 (mitochondrial Slc25a20 1.704 1.697
carnitine/acylcarnitine translocase), member 20 CD36 antigen Cd36
1.584 1.513 phosphoenolpyruvate carboxykinase 1, cytosolic Pck1
3.518 1.781 fatty acid synthase Fasn 6.323 2.24 fatty acid binding
protein 4, adipocyte Fabp4 2.189 1.81 monoglyceride lipase Mgll
1.907 1.51 acetyl-Coenzyme A acetyltransferase 2 Acat2 1.625 1.563
acetyl-Coenzyme A dehydrogenase, long-chain Acadl 2.549 1.992
resistin Retn 4.114 1.756 malonyl-CoA decarboxylase Mlycd 1.781
1.962 transketolase Tkt 2.256 1.983 ATP citrate lyase Acly 2.458
1.91 HEAT SHOCK heat shock protein 90 kDa alpha (cytosolic), class
A member 1 Hsp90aa1 1.455 0.616 DnaJ (Hsp40) homolog, subfamily B,
member 1 Dnajb1 3.59 0.604 CYTOKINES interferon, alpha-inducible
protein 27 Ifi27 1.714 1.537 OTHER sarcolipin Sln 0.363 4.576
thyroid hormone responsive SPOT14 homolog (Rattus) Thrsp 2.685
1.766 RIKEN cDNA 2310076L09 gene 2310076L09Rik 1.868 2.117 myosin,
heavy polypeptide 2, skeletal muscle, adult Myh2 2.194 1.797
surfeit gene 4 Surf4 2.091 0.654 acid phosphatase 5, tartrate
resistant Acp5 3.91 1.477 serine (or cysteine) proteinase
inhibitor, clade A, member 1a Serpina1a 0.396 3.891 cysteine
dioxygenase 1, cytosolic Cdo1 3.266 1.678 erythroid differentiation
regulator 1 0.619 1.805 RIKEN cDNA 1810073N04 gene 1810073N04Rik
2.326 1.628 superoxide dismutase 3, extracellular Sod3 1.606 1.617
complement factor D (adipsin) Cfd 2.828 1.5 cytochrome P450, family
2, subfamily e, polypeptide 1 Cyp2e1 2.941 1.743 catalase Cat 1.728
1.902 early growth response 1 Egr1 2.577 0.65 OXYGEN CARRIER
hemoglobin, beta adult minor chain|hemoglobin Y, beta- Hbb-b2|Hbb-y
1.626 1.503 like embryonic chain STEROID BIOGENESIS retinol binding
protein 4, plasma Rbp4 2.065 2.225 SIGNAL TRANSDUCTION adreneyrgic
receptor, beta 3 Adrb3 3.83 1.56 protein tyrosine phosphatase-like
(proline instead of catalytic Ptplb 2.38 1.569 arginine), member b
dual specificity phosphatase 7 Dusp7 1.661 1.672 TRANSCRIPTION
nuclear receptor subfamily 4, group A, member 2 Nr4a2 1.776 0.437
TRANSPORT solute carrier family 1 (neutral amino acid transporter),
Slc1a5 1.939 1.511 member 5 two pore channel 1 Tpcn1 2.842 1.487
seminal vesicle secretion 5 Svs5 0.095 2.243 Data is average of N =
3 samples in each group (p < 0.05).
[0184] Quantitative expression analysis of selective oxidative
genes (eight of those listed in Table 4) was determined in
quadriceps of mice treated with vehicle (V), GW1516 (GW, 5
mg/kg/day), AICAR (AI, 250 mg/kg/day) and the combination of the
two drugs (GW+AI) for 6 days using the methods described in Example
1. As shown in FIGS. 9A-H, several of these biomarkers including
PDK4, SCD1, ATP citrate lyase, HSL, mFABP and LPL were induced in a
synergistic fashion by GW1516 and AICAR in the quadriceps (FIGS.
9C-9H). Intriguingly, synergism was undetectable in UCP3 and mCPT I
(FIGS. 9A and B). These genes were induced in quadriceps of
untrained VP16-PPAR.delta. mice, where AMPK is constitutively
active (Table 5).
TABLE-US-00006 TABLE 5 Selective oxidative genes induced in muscle
by combined PPAR.delta. and AMPK activation as well as
VP16-PPAR.delta. over-expression Description Locus GW + AI
VP-PPAR.delta. ATP citrate lyase Acly 1.648 3.095 carnitine
palmitoyltransferase 1b, Cpt1b 1.371 1.678 muscle fatty acid
binding protein 3, muscle Fabp3 1.447 5.904 and heart fatty acid
synthase Fasn 2.24 2.749 lipoprotein lipase Lpl 1.113 1.72 lipase,
hormone sensitive Lipe 1.746 2.203 pyruvate dehydrogenase kinase,
Pdk4 2.486 5.06 isoenzyme 4 stearoyl-Coenzyme A desaturase 1 Scd1
1.78 7.353 uncoupling protein 3 Ucp3 2.792 4.107
[0185] Collectively, these results demonstrate that while
interaction between AMPK and PPAR.delta. may substantially
contribute to re-programming of the skeletal muscle transcriptome
during exercise, additional changes may involve cross-talk between
other components of the exercise signaling network and
PPAR.delta..
[0186] In summary, PPAR.delta. and exercise synergistically
regulate running endurance. Although not bound by theory, kinase
activation may influence PPAR.delta. signaling during exercise in
establishing an "endurance gene expression signature" that
effectively enhances performance.
Example 7
AMPK Increases Transcriptional Activation by PPAR.delta.
[0187] The genetic synergism described in Example 6 indicates that
AMPK directly regulates the transcriptional activity of PPAR.delta.
in skeletal muscles. To demonstrate this, an analysis of the
effects of GW1516 and AICAR on gene expression in primary muscle
cells isolated from wild type and PPAR.delta. null mice was
performed.
[0188] Primary muscle cells were isolated from wild type and
PPAR.delta. null mice as previously described (Rando and Blau, J.
Cell. Biol. 125(6):1275-87, 1994). Skeletal muscle C2C12 cells were
cultured in DMEM containing 20% serum and penicillin/streptomycin
cocktail. For differentiation, cells at 80% confluence were
switched to a differentiation medium (DMEM+2% serum) for 4 days to
obtain differentiated myotubules. Cells were treated with vehicle,
GW1516, AICAR, or GW1516+AICAR (GW: 0.1 .mu.M; AICAR: 500 .mu.M)
for 24 hours. RNA expression of UCP3, PDK4, LPL, and HSL was
determined using real time quantitative PCR as described in Example
1.
[0189] As shown in FIGS. 10A-D, synergism is dependent on
PPAR.delta. and lost in the null cells. Similar synergistic
regulation of gene expression by GW1516 and AICAR was also observed
in differentiated C2C12 cells. These results show that AMPK
activation may enhance ligand-dependent transcriptional effects of
PPAR.delta. in muscles.
[0190] To more directly address this, reporter gene expression
assays were utilized. AD 293 cells were cultured in DMEM containing
10% serum and an antibiotic cocktail. Cells were transfected with
one or more of CMX-Flag, CMX-Flag PPAR.delta., CMX-Tk-PPRE, or
CMX-.beta.GAL, or an hAMPK (.alpha.1 and .alpha.2 subunits,
Origene) expression vector using Lipofectamine.TM. 2000 in
accordance with the manufacturer's instructions. Anti-Flag
antibody-conjugated beads were incubated overnight at 4.degree. C.
with lysates from transfected cells. Flag-tagged protein or protein
complexes were immunoprecipitated by separating the beads from
non-bound materials. The beads were washed in ice-cold lysis buffer
followed by extraction in Laemmli buffer. For
co-immunoprecipitation experiments SDS was excluded from the lysis
buffer. Western blotting was performed with antibodies specific for
the Flag tag or AMPK .alpha. subunit(s).
[0191] Co-transfection of either catalytic AMPK .alpha.1 or
.alpha.2 subunits, but not control vector, with PPAR.delta.
increased the basal (FIG. 10E) and GW1516-dependent transcriptional
activity (FIG. 10F) of PPAR.delta. in inducing a PPRE-driven
reporter gene in AD293 cells. AMPK over-expression or GW1516
treatment did not change reporter activity in transfections
excluding the PPAR.delta. expression vector negating the
possibility of an effect via RXR. Additional results indicate that
AMPK may modulate PPAR.delta. transcriptional activity by directly
interacting with the receptor. In AD293 cells co-transfected with
Flag-PPAR.delta. and with either catalytic AMPK .alpha.1 or
.alpha.2 subunits, both of the subunits co-immunoprecipitated as a
complex with Flag-PPAR.delta. (FIG. 10G). Furthermore,
Flag-PPAR.delta. also co-immunoprecipitated endogenous AMPK.alpha.
subunits from AD293 cells confirming a direct physical interaction
between the nuclear receptor and the kinase (FIG. 10H). Despite
physical interaction, AMPK failed to increase PPAR.delta.
phosphorylation.
[0192] While potential AMPK phosphorylation sites were found in
PPAR.delta., none of these sites were phosphorylated by AMPK in in
vitro kinase assays. This was further confirmed by measuring the
p32 labeling of PPAR.delta. in AD 293 cells in the presence or
absence of AMPK. AD 293 cells were transfected with PPAR.delta. and
hAMPk (.alpha.1 or .alpha.2 subunit) expression vectors as
described above. Forty-eight hours after transfection, the cells
were washed three times with phosphate-free DMEM and incubated with
.sup.32P-orthophosphate in phosphate-free DMEM for 20 hours (100
.mu.Ci/5 ml). Cells were washed three times with ice-cold
phosphate-free DMEM and lysed in ice-cold lysis buffer.
[0193] As shown in FIG. 10I, overall PPAR.delta. phosphorylation is
not increased by AMPK in vivo. However, co-transfection of
AMPK.alpha.2 and co-activator PGC1.alpha. (a known phosphorylation
target of AMPK) co-operatively interact to further induce both the
basal and ligand-dependent transcriptional activity of PPAR.delta.
(FIG. 10J). Strikingly, no significant physical interaction between
Flag-PGC1.alpha. and AMPK (FIG. 10K) was detected, both of which
independently interacted with PPAR.delta.. Collectively, these
observations indicate that AMPK may be present in a transcriptional
complex with PPAR.delta. where it can potentiate receptor activity
via direct protein-protein interaction and/or by phosphorylating
co-activators such as PGC1.alpha..
[0194] These results indicate that AMPK directly interacts with
PPAR.delta. and dramatically increases basal and ligand-dependent
transcription via the receptor. Despite physical interaction, AMPK
does not phosphorylate PPAR.delta.. AMPK and its substrate
PGC1.alpha. synergistically increased PPAR.delta. transcription,
indicating indirect regulation of receptor by AMPK via co-regulator
modification.
[0195] The conclusion that exercise-activated AMPK interacts with
PPAR.delta. in regulating gene expression in vivo is strengthened
by the observation that treatment of animals with AICAR (AMPK
activator) and GW1516 creates a gene signature in skeletal muscle
that replicates up to 40% of the genetic effects of combined
exercise and GW1516 treatment (see Table 4). Moreover, several
candidate genes from this signature are synergistically induced by
GW1516 and AICAR in wild type but not in PPAR.delta. null primary
muscle cells, demonstrating that the interactive effects of the two
drugs are mediated through PPAR.delta.. While 45% of the commonly
regulated genes are linked to oxidative metabolism, additional
common targets relevant to muscle performance include angiogenic,
signal transduction and glucose sparing genes (Table 4). It is
possible that the portion of the PPAR.delta.-exercise signature
that is independent of PPAR.delta.-AMPK interaction (FIG. 8B) may
depend on cross-talk between the receptor and other exercise signal
transducers such as MAPK, calcineurin/NFAT and SIRT 1. These
possibilities are summarized in FIG. 10L, where AMPK and additional
components of the signaling network are proposed to interact with
liganded PPAR.delta. to generate a muscle endurance gene signature
and enhanced endurance adaptation.
[0196] In summary, it is shown herein that synthetic PPAR.delta.
activation alone induces a set of genomic changes that fail to
alter the preset muscle architecture and endurance levels in adult
mice. However, the combination of PPAR.delta. activation with
exercise brings about novel transcriptional changes, potentially
via interaction with kinases such as AMPK (as depicted in FIG.
10L), re-setting the muscle transcriptome to a phenotype that
dramatically enhances muscle performance.
Example 8
Enhancing Exercise Effect in a Subject
[0197] This example describes methods that can be used to increase
or enhance an exercise in a healthy mammalian subject. Although
specific conditions are described, one skilled in the art will
appreciate that minor changes can be made to such conditions.
[0198] Healthy adult human subjects perform aerobic exercise (e.g.,
running) for at least 30 minutes (e.g., 30-90 minutes) for at least
3-4 days per week (e.g., 3-7 days per week) for at least 2 weeks
(e.g., at least 4-12 weeks). The exercise is performed at 40%-50%
maximal heart rate, 50%-60% maximal heart rate, 60%-70% maximal
heart rate, or 75%-80% maximal heart rate, where maximum heart rate
for a human subject is calculated as: 220 bps-(age of the
subject).
[0199] During or after performing aerobic exercise as described
above, the subjects are orally administered GW1516
[(2-methyl-4(((4-methyl-2-(4-trifluoromethylphenyl)-1,3-thiazol-5-yl)meth-
yl)sulfanyl)phenoxy)acetic acid] at a dose of 1 to 20 mg per day,
such as 2.5 or 10 mg per day. Subjects can continue to perform
aerobic exercise while receiving GW1516. The subject can receive
GW1516 for a period of at least 2 weeks, such as at least 4
weeks.
[0200] The exercise effect achieved in the treated subjects (e.g.,
running endurance) can be compared to such an effect in untreated
subjects. Exercise effect can be measured using methods known in
the art, such as measuring aerobic or running endurance (for
example measuring distance run until exhaustion or amount of time
to run a particular distance). In some instances, the exercise
effect of interest is increased in treated subjects by at least 5%,
such as at least 10% as compared to untreated subjects.
Example 9
Identifying Performance Enhancing Substances in an Exercise-Trained
Subject
[0201] This example describes methods that can be used to identify
performance-enhancing substances in an exercised-trained
subject.
[0202] A biological sample obtained from a healthy adult human is
analyzed to determine if the subject is taking a PES (e.g., GW1516)
by analyzing expression of one or more of the molecules (nucleic
acids or proteins) listed in Table 2 or Table 4. Suitable
biological samples include samples containing genomic DNA or RNA
(including mRNA) or proteins obtained from cells of a subject, such
as those present in peripheral blood, urine, saliva, tissue biopsy,
or buccal swab. For example, a biological sample of the subject can
be assayed for a change in expression (such as an increase or
decrease) of any combination of at least four molecules (nucleic
acids or proteins) listed in Table 2 or 4, such as any combination
of at least 10, at least 20, at least 30, or at least 40 of those
listed in Table 2 or 4, for example all of those listed in Table 2
or 4.
Analyzing Nucleic Acid Molecules
[0203] Methods of isolating nucleic acid molecules from a
biological sample are routine, for example using PCR to amplify the
molecules from the sample, or by using a commercially available kit
to isolate mRNA or cDNA. However, nucleic acids need not be
isolated prior to analysis. Nucleic acids can be contacted with an
oligonucleotide probe that will hybridize under stringent
conditions with one or more nucleic acid molecule listed in Table 2
or 4. The nucleic acids which hybridize with the probe are then
detected and quantified. The sequence of the oligonucleotide probe
can bind specifically to a nucleic acid molecule represented by the
sequences listed in Table 2 or 4.
[0204] Increased or decreased expression of the molecules listed in
Table 2 or 4 can be detected by measuring the cellular levels of
mRNA. mRNA can be measured using techniques well known in the art,
including for instance Northern analysis, RT-PCR and mRNA in situ
hybridization. Details of mRNA analysis procedures can be found,
for instance, in provided examples and in Sambrook et al. (ed.),
Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.
[0205] Oligonucleotides specific to sequences listed in Table 2 or
4 can be chemically synthesized using commercially available
machines. These oligonucleotides can then be labeled, for example
with radioactive isotopes (such as .sup.32P) or with
non-radioactive labels such as biotin (Ward and Langer et al.,
Proc. Natl. Acad. Sci. USA 78:6633-57, 1981) or a fluorophore, and
hybridized to individual DNA samples immobilized on membranes or
other solid supports by dot-blot or transfer from gels after
electrophoresis. These specific sequences are visualized, for
example by methods such as autoradiography or fluorometric
(Landegren et al., Science 242:229-37, 1989) or calorimetric
reactions (Gebeyehu et al., Nucleic Acids Res. 15:4513-34,
1987).
Analyzing Proteins
[0206] Proteins in the biological sample can also be analyzed. In
some examples, proteins are isolated using routine methods prior to
analysis.
[0207] In one example, surface-enhanced laser desorption-ionization
time-of-flight (SELDI-TOF) mass spectrometry is used to detect
changes in differential protein expression, for example by using
the ProteinChip.TM. (Ciphergen Biosystems, Palo Alto, Calif.). Such
methods are well known in the art (for example see U.S. Pat. No.
5,719,060; U.S. Pat. No. 6,897,072; and U.S. Pat. No. 6,881,586).
SELDI is a solid phase method for desorption in which the analyte
is presented to the energy stream on a surface that enhances
analyte capture or desorption. Therefore, in a particular example,
the chromatographic surface includes antibodies that recognize
proteins listed in Table 2 or 4. Antigens present in the sample can
recognize the antibodies on the chromatographic surface. The
unbound proteins and mass spectrometric interfering compounds are
washed away and the proteins that are retained on the
chromatographic surface are analyzed and detected by SELDI-TOF. The
MS profile from the sample can be then compared using differential
protein expression mapping, whereby relative expression levels of
proteins at specific molecular weights are compared by a variety of
statistical techniques and bioinformatic software systems.
[0208] In another examples, the availability of antibodies specific
to the molecules listed in Table 2 or 4 facilitates the detection
and quantification of proteins by one of a number of immunoassay
methods that are well known in the art, such as those presented in
Harlow and Lane (Antibodies, A Laboratory Manual, CSHL, New York,
1988). Methods of constructing such antibodies are known in the
art. Any standard immunoassay format (such as ELISA, Western blot,
or RIA assay) can be used to measure protein levels.
Immunohistochemical techniques can also be utilized for protein
detection and quantification. For example, a tissue sample can be
obtained from a subject, and a section stained for the presence of
the desired protein using the appropriate specific binding agents
and any standard detection system (such as one that includes a
secondary antibody conjugated to horseradish peroxidase). General
guidance regarding such techniques can be found in Bancroft and
Stevens (Theory and Practice of Histological Techniques, Churchill
Livingstone, 1982) and Ausubel et al. (Current Protocols in
Molecular Biology, John Wiley & Sons, New York, 1998).
[0209] For the purposes of detecting or even quantifying protein or
nucleic acid expression, expression in the test sample can be
compared to levels found in cells from a subject who has not taken
a PES. Alternatively, the pattern of expression identified in the
test subject can be compared to that shown in Table 2 or 4.
[0210] For example, if the test sample shows a pattern of
expression similar to that in Table 2 or 4 (e.g. the genes shown as
upregulated and downregulated in Table 2 or 4 are observed in the
subject to be upregulated and downregulated, respectively), this
indicates that the subject is taking a PES, such as a PPAR.delta.
agonist (e.g. GW1516). In contrast, If the pattern of expression
identified in the test subject is different to that shown in Table
2 or 4 (e.g. the genes shown as upregulated and downregulated in
Table 2 or 4 are observed in the subject to be not differentially
expressed or show a different pattern of regulation), this
indicates that the subject is not taking a PES, such as a
PPAR.delta. agonist (e.g. GW1516).
[0211] A significant increase in the non-bolded proteins listed in
Table 2 in the cells of a test subject compared to the amount of
the same protein found in normal human cells is usually at least
2-fold, at least 3-fold, at least 4-fold or greater difference.
Substantial overexpression of the non-bolded proteins listed in
Table 2 in the subject's sample can be indicative of the subject
taking a PES. Similarly, a significant decrease in the bolded
proteins listed in Table 2 in the cells of a test subject compared
to the amount of the same protein found in normal human cells is
usually at least 2-fold, at least 3-fold, at least 4-fold or
greater difference. Substantial underexpression of the bolded
proteins listed in Table 2 in the subject's sample can be
indicative of the subject taking a PES.
[0212] While this disclosure has been described with an emphasis
upon particular embodiments, it will be obvious to those of
ordinary skill in the art that variations of the particular
embodiments may be used and it is intended that the disclosure may
be practiced otherwise than as specifically described herein.
Accordingly, this disclosure includes all modifications encompassed
within the spirit and scope of the disclosure as defined by the
following claims:
* * * * *