WO2023059590A1

WO2023059590A1 - Compositions and methods for treating metabolic disease

Info

Publication number: WO2023059590A1
Application number: PCT/US2022/045615
Authority: WO
Inventors: Zhenqi ZHOU
Original assignee: University of California Berkeley; University of California San Diego UCSD
Current assignee: University of California Berkeley; University of California San Diego UCSD
Priority date: 2021-10-05
Filing date: 2022-10-04
Publication date: 2023-04-13
Anticipated expiration: 2024-04-05
Also published as: EP4412632A4; US20250339501A1; EP4412632A1

Abstract

The present disclosure relates to compositions and methods for treaty obesity-related diseases. In some aspects, methods are provided for increasing the expression and/or activity of Dj 1 protein in a subject in need thereof.

Description

COMPOSITIONS AND METHODS FOR TREATING METABOLIC DISEASE

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Patent Application No. 63/252,443, filed on October 5, 2021, which is hereby incorporated by reference in its entirety.

STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH

This invention was made with government support under Grant No. DK063491 awarded by the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND

Metabolic dysfunction, manifested clinically as metabolic syndrome, has become a global epidemic that dramatically increases the risk of non-alcoholic fatty liver disease (NAFLD), type 2 diabetes, and cardiovascular disease (CVD). Elevated hepatic glucose production and lipoprotein secretion contribute to the pathogenesis of hyperglycemia and hyperlipidemia in insulin resistance, and obesity is associated with excess fat accumulation in the liver, a defining feature of NAFLD that affects one-third of adults and an increasing number of children in developed countries (1). NAFLD refers to a group of related disorders increasing in severity from hepatic steatosis, nonalcoholic steatohepatitis (NASH), cirrhosis, and ultimately hepatocarcinomas (1,2). Although combination and single drug therapies are under evaluation, no pharmacological treatment is approved for NAFLD (2). Hence, understanding the molecular mechanisms underlying NAFLD and hormonal cues that mediate the crosstalk among different tissues, particularly between skeletal muscle and the liver are urgent for the development of effective therapies.

The foregoing observations provide evidence of the continuing need for compositions and formulations useful in treating metabolic dysfunction diseases, such as type 2 diabetes, cardiovascular disease, and NAFLD. SUMMARY OF THE INVENTION

The invention features compositions and methods that are useful for diagnosing muscle injury and treating metabolic diseases and disorders. The invention is based, at least in part, on the discovery that skeletal muscle releases Dj 1 protein in extracellular vesicles and that Dj 1 enhances fatty acid oxidation, decreases lipid content, improves mitochondrial function, and suppresses the ASKl-JNK-PPARa signaling in the liver and improves glucose homeostasis in non-alcoholic steatohepatitis in mice.

Accordingly, one aspect of the invention provides a method of treating a metabolic disease or disorder or symptom thereof, comprising administering to a patient in need thereof a therapeutically effective amount of a Dj 1 polypeptide or a fragment thereof or polynucleotide encoding a Dj 1 polypeptide or a fragment thereof. The metabolic disorder can be selected from non-alcoholic fatty liver disease (NAFLD), steatohepatitis, type II diabetes, hyperglycemia, hyperlipidemia, dyslipidemia, obesity, hyperinsulinemia, insulin resistance, hypercholesterolemia, non-familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, atherosclerosis, early onset coronary heart disease, dyslipidemia, hypertriglyceridemia, hyperfattyacidemia, and cirrhosis. The fragment of the Dj 1 polypeptide can comprise residues 32-173. The Dj 1 polypeptide or polypeptide or fragment thereof can be purified and/or isolated from recombinant sources.

BRIEF DESCRIPTION OF THE DRAWINGS

Figures 1A-1Q show that skeletal muscle injury elevates the circulating levels of Dj 1. Figures 1A and IB show circulating levels of Dj l and CKMB, respectively, of 2 and 4 weeks-old mdx mice (n=8-10). Figures 1C shows plasma Dj 1 levels of the mice after downhill running (DHR) at the indicated time vs. the sedentary mice (SED) (n=7-12). Figure ID shows that the circulating levels of Dj 1 from CTX-injected wild-type mice (WT) were analyzed via immunoblotting. The bar graph on the right is the protein densitometry analysis of Dj 1 in the plasma (n=5). Figure IE shows plasma Dj 1 levels of WT mice intramuscularly (IM) injected with CTX (Day 2 post-injection). Figure IF shows an immunoblot analysis of Dj 1 protein in the raw culture medium (medium only) and the culture medium of primary mouse myotubes and C2C12 myotubes (n=3). Figure 1G comprises immunoblot analyses of Dj 1 protein in C2C12 myocytes and 3T3-L1 preadipocytes that were transduced with adenovirus encoding a Dj 1 protein at the indicated dosage and in the cell media of these cultures. Figure 1H is an immunoblot analysis of Dj 1 protein in C2C12 myocytes treated with carbonyl cyanide m-chlorophenyl hydrazine (CCCP) at the indicated time and an immunoblot showing the Dj 1 protein level in the culture medium. Figure II is an immunoblot analysis of Dj 1 protein level in C2C12 myocytes and in the culture media with and without CCCP treatment. Figure 1J is a graph showing the circulating Dj l protein level in male wild-type mice at the indicated age (n=5-10). Figure IK is a plot showing the plasma Dj 1 levels of WT mice that underwent acute exercise or exercise training and WT mice that were kept sedentary (n=5-10). Figure IL includes images of H & E staining of gastrocnemius muscle sections from 2-week-old and 4-weeks old WT mice and mdx mice. Figure IM is an immunoblot analysis of Dj 1 protein level in skeletal muscle of 2-week-old WT mice and mdx mice (n=6-8). Figure IN shows images of H & E staining of gastrocnemius muscle from WT mice injected with saline or CTX (n=6). Figure 10 is an immunoblot analysis of the Dj 1 protein levels of gastrocnemius muscle from WT mice injected saline or CTX (n=6). Figures 1P-1Q show skeletal muscle is the primary source of circulating Dj l. Figure IP is an immunoblot analysis of the Dj 1 protein levels of gastrocnemius muscle from Control f/f vs. mPark7^K0 mice (n=4). Figure IQ shows the plasma Dj 1 levels in Control f/f vs. mPark7^K0 mice (n=12-14). Values are mean ± SEM, * = p<0.05.

Figures 2A-2L show that endoplasmic reticulum (ER) stress stimulates muscle cells release of Dj 1. Figure 2A shows an immunoblotting analysis of ER stress markers in quadriceps muscle of WT and mdx mice (n=5-6). Bar graphs on the right shows the densitometry of ER stress markers that were normalized to GAPDH. Figure 2B and 2C are the protein levels and the gene expression of ER stress markers in the quadriceps muscle of the SED and downhill-running (DHR) C57BL/6J mice (n=6). Figure 2D is an immunoblot analysis of ER stress marker expression in C57BL/6J mice that were administered with vehicle or 10 pM CTX (n=6). Bar graphs on the right shows the densitometry of ER stress markers that were normalized to GAPDH. Figure 2E is a plot showing the protein levels of Dj 1 in the cell culture medium from C2C12 myotubes treated with vehicle, thapsigargin (Tg), CCCP, or antimycin A (n=4). Figure 2F is a plot showing the protein levels of Dj 1 in the Krebs-Hensel eit buffer (KHB) only and the KHB medium of EDL muscle treated with vehicle or Tg (n=6). Figure 2G is a plot showing the relative Dj 1 levels in the medium of C2C12 myotubes treated with vehicle, CCCP, CCCP+GW4869, Tg, Tg+GW4869, or GW4869 (n=4). Figure 2H is a plot showing the relative Dj 1 levels in the medium of C2C12 myotubes treated with vehicle, CCCP, CCCP+Exol, Tg, Tg+Exol, or Exol (n=4-6). Figure 21 is time-lapse images of Dj 1-GFP overexpressed C2C12 myocytes treated with Tg or CCCP. Figure 2J is a schematic of an experimental design to separate multivesicular bodies (MVBs) and exosomes from the cell culture medium. The immunoblot analysis shows that Dj 1 protein is enriched in the multivesicular bodies (MVBs) of the cell medium from C2C12 myotubes treated with Tg. Figure 2K is an immunoblot analysis showing that Dj 1 was detected in both MVBs and exosomes of WT mice plasma. Figure 2L is a plot showing Dj 1 protein level in the Krebs-Henseleit buffer (KHB) only and the KHB medium of soleus (SOL) muscle treated with vehicle or Tg (n=4-6). Values are mean ± SEM, * = p<0.05.

Figures 3A-3N show that Dj 1 targets the liver and kidneys of the mice. Figure 3 A shows intravital imaging of WT mice that were administered with IRDye 800CW-labeled Dj 1 via tail vein (IV) injection. Figures 3B and Figure 3C show images and region of interest (ROI) quantification, respectively, of IRDye 800CW-labeled Dj 1 signals in organs. Figure 3D shows fluorescent imaging of AML 12 mouse liver cells treated with GFP or Alexa Fluor 488 labeled Dj 1 protein (without wash). Plasma membranes were stained with Wheat Germ Agglutinin conjugated to Alexa Fluor 594. Nuclei were stained with DAPI. Figure 3E is a immunoblot analysis showing that recombinant human Dj 1 protein activates the phosphorylation of AMPK and ACC in HepG2 cells (n=3). Figure 3F is a plot showing recombinant human Dj 1 protein enhances OCR/ECAR ratio. Figure 3G is a graph showing recombinant human Dj 1 protein enhances ATP production from mitochondria (n=6-8). Figure 3H shows an Ingenuity Pathway Analysis (IP A) of RNA sequencing data of HepG2 cells treated with saline or tDj 1 (n=4). Figure 31 shows Coomassie blue staining of purified His-rDj 1 protein (the second lane from right). Figure 3 J shows imaging of IRDye 800CW- labeled Dj 1 protein in a tube. Figure 3K shows imaging of dissected organs from mice injected with saline (left dish) and IRDye 800CW-labeled Dj 1 (right two dishes). Figure 3L is an immunoblot analysis of phosphorylated and total AMPK and ACC in HepG2 cells treated with His-Dj 1 protein at the indicated dosage (n=3). Figure 3M is an immunoblot analysis of phosphorylated and total AMPK in primary mouse hepatocytes treated with His-Dj 1 protein at the indicated time (n=3). Figure 3N is an immunoblot analysis of phosphorylated and total AMPK in HepG2 cells treated with GFP or His-Dj 1 protein at the indicated dosage and time (n=3). Values are mean ± SEM, * = p<0.05.

Figures 4A-4GG show that Dj 1 administration improves lipid metabolism and glucose homeostasis. Figure 4A is a graph quantifying fatty acid oxidation in HepG2 cells treated with saline or recombinant human Dj 1 protein (rDj 1) (n=4). Figure 4B is a graph quantifying Oil red O staining of HepG2 cells treated with rDj 1 at the indicated time (n=4). Figure 4C shows the triacylglycerol (TG) level in HepG2 cells cultured in low glucose medium (Control), high-fat high-glucose (HFHG), and high-fat high-glucose plus rDj 1 (HFHD+rDj 1) (n=6-8). The data presented in Figures 4D-4I are from experiments with C57BL/6J mice that were administered mouse recombinant Dj 1 (rDj 1) protein (0.15 mg/kg/day via IV for 5 days; n=5). Figure 4D is a graph showing plasma NEFA levels. Figure 4E is a graph showing plasma cholesterol levels. Figure 4F is a graph showing plasma TG levels. Figure 4G is a graph showing liver NEFA. Figure 4H is a graph showing liver cholesterol levels. Figure 41 is a graph showing liver TG levels. Figure 4J includes images of H & E staining of liver sections from NC or HFD- fed mice injected with saline or rDj 1. The data presented in Figures 4K-4M are from experiments with HFD-fed C57BL/6J mice that were administered with rDj 1 (0.15 mg/kg/day; IV) for 5 days (n=10-l 1). Figure 4K is a graph quantifying the results of a glucose tolerance test of the HFD-fed C57BL/6J mice after treatment. Figure 4L is a graph quantifying the results of an insulin tolerance test of the HFD-fed C57BL/6J mice after treatment. Figure 4M is a graph showing the body weight of the HFD-fed C57BL/6J mice after treatment. The data presented in Figures 4N-4S are from experiments on HFD-fed mice that were administered with either saline or rDj 1 (n=4-5). Figure 4N is a graph showing oxygen consumption (VO2) in the HFD- fed mice. Figure 40 is a graph showing CO2 production (VCO2) in the HFD-fed mice. Figure 4P is a graph showing energy expenditure (EE) in the HFD-fed mice. Figure 4Q is a respiratory exchange ratio (RER) in the HFD-fed mice. Figure 4R and Figure 4S are graphs showing mitochondrial complex I and complex II activity, respectively, of isolated mitochondria from the liver of the HFD-fed mice treated with saline vs. rDj 1 (n=5). Figure 4T is an image of mice that were administered with saline or rDj 1. Figure 4U is a graph showing fasting blood glucose levels of NC-fed mice that were administered with saline or rDj 1 via IV injection (n=5). Figure 4V is a graph showing lactate concentration in lactate of NC-fed mice that were administered with saline or rDj 1 via IV injection (n=5). Figure 4W is a graph of body weight of NC-fed mice that were administered with saline or rDj 1 (n=5). Figure 4X is a graph of fasting blood glucose levels of HFD-fed mice that were administered with saline or rDj 1 (n=5). Figure 4Y is a graph showing lactate concentration in lactate of HFD-fed mice that were administered with saline or rDj 1 (n=5). Figure 4Z is a graph showing body weight of HFD-fed mice administered with saline or rDj 1 (n=5). The data presented in Figures 4AA- 4GG were obtained from experiments in HFD-fed mice that were administered with saline or rDj 1 (n=4-5). Figure 4AA is a graph showing oxygen consumption (VO2) in the HFD-fed mice. Figure 4BB is a graph showing CO2 production (VCO2) in the HFD-fed mice. Figure 4CC is a graph showing energy expenditure (EE) in the HFD-fed mice. Figure 4DD is a graph showing respiratory exchange ratio (RER) of the HFD-fed mice. Figure 4EE is a graph showing food consumption in the HFD-fed mice. Figure 4FF is a graph showing water consumption in the HFD-fed mice. Figure 4GG is a graph showing total activity of the HFD- fed mice. Values are mean ± SEM, * = p<0.05.

Figures 5A-5S show that Dj 1 administration reduces hepatic steatosis. Figures 5A-5F are graphs comparing biomarker levels in HFD-fed mice administered with saline, rDj l, or tDj 1 (n=6-10). Figure 5 A is a graph showing plasma NEFA levels. Figure 5B is a graph showing plasma cholesterol levels. Figure 5C is a graph showing plasma triglyceride levels. Figure 5D is a graph showing liver NEFA levels. Figure 5E is a graph showing liver cholesterol levels. Figure 5F is a graph showing liver triglyceride levels. Figure 5G is an image of HFD-fed mice that were administered with saline or rDj l. Figure 5H is an image of HFD-fed mice that were administered with saline or tDj 1. Figure 51 is an image of the liver from HFD-fed mice that were administered with saline or tDj 1. Figure 5 J includes images of H & E staining of liver sections from HFD-fed mice that were administered with saline, rDj l, or tDj 1. Figure 5K is a graph of aspartate aminotransferase (AST) activity in the liver of HFD-fed mice (n=5-17) that were administered with saline, rDj l, or tDj 1 via injection. Figure 5L is a graph alanine transaminase (ALT) activity in the liver of HFD-fed mice (n=5-17) that were administered with saline, rDj l, or tDj 1 via tail-vein injection. Figure 5M is a graph showing TG levels in AML12 cells treated with saline+PA or tDj 1+PA (n=3). Figure 5N is a graph of NEFA content in AML 12 cells treated with saline+PA or tDj 1+PA (n=3). Figure 50 is a Coomassie blue staining of purified His-tDj 1 protein. Figure 5P are the images of the liver from HFD-fed mice administered with saline or tDj 1. Figure 5Q is a graph showing the average liver weight of HFD-fed mice treated with saline or tDj 1. Figure 5R is a graph of body weight of HFD-fed mice during the rDj 1 injection (n=5-6). Figure 5S is a graph showing ALT activity in the liver of NC-fed mice treated with saline or rDj 1 (n=5). Values shown in Figures 5A-5F, 5K-5N, and 5Q-5S are mean ± SEM, * = p<0.05, ** = p<0.01.

Figures 6A-6U show that both rDj 1 and truncated Dj 1 (tDj 1) impact hepatic metabolism through the ASKl-JNK-PPARa pathway. Figure 6A and Figure 6B are immunoblot analyses of the protein levels in the JNK (p-54 and p-46) and p38 MAPK pathways, respectively, in HFD-fed mice (n=5) that were administered with saline, rDj l, or tDj 1. Figure 6C shows that rDj 1 inhibits TNFa-induced JNK phosphorylation in HepG2 cells (n=3). Figure 6D shows that tDj 1 inhibits Anisomycin-induced JNK phosphorylation in AML12 cells (n=3). Figure 6E shows that tDj 1 inhibits the phosphorylation of ASK1, but not TAK1 in the liver of HFD-fed WT mice (n=5). The bar graph at the bottom is the protein densitometry analysis. Figure 6F is a graph showing the relative amount of reactive oxygen species (ROS) in HepG2 cells treated with vehicle, rDj 1, TNFa, or TNFa+rDj 1 (n=6). Figure 6G is a graph showing proinflammatory cytokine gene expression in the liver of HFD-fed mice that were administered with saline or rDj 1 (n=5-6). Figure 6H and Figure 61 are graphs showing gene expression in the liver of NC-fed mice (n=5-7) and HFD-fed mice (n=10), respectively, that were treated with saline or rDj 1. Figure 6 J and Figure 6K are immunoblot analyses of PPARa expression in the liver of NC-fed mice (n=5) and HFD-fed mice (n=5-6), respectively, that were treated with saline or rDj 1. Figure 6L and Figure 6M are graphs showing PPARa transcriptional activity in the liver of NC-fed mice (n=5-6) and HFD-fed mice (n=9-10), respectively, that were treated with saline or rDj 1 (n=9-10). Figure 6N is a graph showing the plasma beta-hydroxybutyrate level of NC-fed mice (n=5). Figure 60 is an immunoblot analysis of p-p42/t-p42 and p-AMPK/t-AMPK in the liver of HFD-fed mice treated with saline or tDj 1 (n=5-6). Figure 6P shows phosphorylated and total ASK1 protein levels in HepG2 cells treated with saline or rDj 1. Figure 6Q is an immunoblot analysis of Eif2a, cleaved caspase 3, and ACC in the liver of HFD-fed mice treated with saline or tDj 1 (n=5-6). Figure 6S is an immunoblot analysis of autophagy and lipid metabolism proteins in the liver of 8 wks and 12 wks HFD-fed mice treated with saline or rDj 1 (n=5-6). Figure 6T is an immunoblot analysis of the autophagy and lipid metabolism proteins in the liver of 12 wks HFD-fed mice treated with saline or rDj 1 (n=5-6). Figure 6U is a graph showing the plasma beta-hydroxybutyrate level of the HFD-fed mice treated with saline or rDj 1 (n=10-l 1). Values are mean ± SEM, * = p<0.05.

Figures 7A-7X show that Dj 1 improves glucose and insulin sensitivity and suppresses inflammation and apoptosis in the liver of diet-induced mouse NASH model. The data presented in Figures 7A-7M were obtained from NASH diet-fed mice (n=5-10) treated with saline or tDj 1. Figure 7A is a graph showing the change of body weight in these mice. Figure 7B is a graph quantifying glucose tolerance in these mice. Figure 7C is a graph quantifying insulin tolerance in these mice. Figure 7D includes the images of H & E stained liver tissues obtained from these mice. Figure 7E includes the images of liver tissues obtained from these mice and stained with Masson’s tri chrome. Figure 7F includes images of liver tissues obtained from these mice and labeled with fluorescently labeled anti-F4/80 antibodies and DAPI stained. Figure 7G includes images of liver tissues obtained from these mice and subjected to TUNEL and DAPI staining. Figure 7H is a graph showing liver cholesterol levels in the NASH diet-fed mice treated with saline or tDj 1 (n=5). Figure 71 is a graph showing ALT activity in the liver of these mice (n=5). Figure 7J is a graph showing the liver fibrosis score (n=l 1). Figure 7K is a graph showing the percentage area fraction of liver fibrosis for these mice (n=5). Figure 7L is a graph showing a qPCR analysis of inflammation and fibrosis gene expression in the liver of NASH diet-fed mice treated with saline or tDj 1 (n=5-l 1). Figure 7M is an immunoblotting analysis of apoptosis markers. Figure 7N, Figure 70, Figure 7P, Figure 7Q, Figure 7R, Figure 7S, and Figure 7T are graphs showing plasma NEFA, plasma TG, liver NEFA, liver TG, plasma cholesterol, AST activity, and tissue weight/body weight ratio of NASH diet-fed mice treated with saline or rDj 1 (n=5). Values are mean ± SEM, * = p<0.05.

DETAILED DESCRIPTION

The invention features compositions and methods that are useful for diagnosing muscle injury and treating metabolic diseases and disorder, such as non-alcoholic fatty liver disease (NAFLD), steatohepatitis, type II diabetes, hyperglycemia, hyperlipidemia, dyslipidemia, obesity, hyperinsulinemia, insulin resistance, hypercholeste rolemia, non- familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, atherosclerosis, early onset coronary heart disease, dyslipidemia, hypertriglyceridemia, hyperfattyacidemia, and cirrhosis. The invention is based, at least in part, on the discovery that skeletal muscle releases of Dj 1 in extracellular vesicles and that Dj 1 enhances fatty acid oxidation, decreases lipid content, improves mitochondrial function, and suppresses the ASK1-JNK signaling in the liver and improves glucose homeostasis in non-alcoholic steatohepatitis in mice.

Definitions

Unless otherwise defined herein, scientific and technical terms used in this application shall have the meanings that are commonly understood by those of ordinary skill in the art. Generally, nomenclature used in connection with, and techniques of, chemistry, cell and tissue culture, molecular biology, cell and cancer biology, neurobiology, neurochemistry, virology, immunology, microbiology, pharmacology, genetics and protein and nucleic acid chemistry, described herein, are those well-known and commonly used in the art. The methods and techniques of the present disclosure are generally performed, unless otherwise indicated, according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout this specification. See, e.g. “Principles of Neural Science”, McGraw-Hill Medical, New York, N.Y. (2000); Motulsky, “Intuitive Biostatistics”, Oxford University Press, Inc. (1995); Lodish et al., “Molecular Cell Biology, 4th ed ”, W. H. Freeman & Co., New York (2000); Griffiths et al., “Introduction to Genetic Analysis, 7th ed ”, W. H. Freeman & Co., N.Y. (1999); and Gilbert et al., “Developmental Biology, 6th ed ”, Sinauer Associates, Inc., Sunderland, MA (2000).

Chemistry terms used herein, unless otherwise defined herein, are used according to conventional usage in the art, as exemplified by “The McGraw-Hill Dictionary of Chemical Terms”, Parker S., Ed., McGraw-Hill, San Francisco, C.A. (1985).

All of the above, and any other publications, patents and published patent applications referred to in this application are specifically incorporated by reference herein. In case of conflict, the present specification, including its specific definitions, will control.

By “agent” is meant a peptide, nucleic acid molecule, or small compound.

By “ameliorate” is meant decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease.

By “alteration” is meant a change (increase or decrease) in the expression levels or activity of a gene or polypeptide as detected by standard art known methods such as those described herein. As used herein, an alteration includes a 10% change in expression levels, preferably a 25% change, more preferably a 40% change, and most preferably a 50% or greater change in expression levels. “

In this disclosure, “comprises,” “comprising,” “containing,” and “having” and the like can have the meaning ascribed to them in U.S. Patent law and can mean “ includes,” “including,” and the like; “consisting essentially of’ or “consists essentially” likewise has the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.

“Detect” refers to identifying the presence, absence, or amount of the analyte to be detected. By “detectable label” is meant a composition that when linked to a molecule of interest renders the latter detectable via spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include radioactive isotopes, magnetic beads, metallic beads, colloidal particles, fluorescent dyes, electron-dense reagents, enzymes (for example, as commonly used in an ELISA), biotin, digoxygenin, or haptens.

“Dj 1 polynucleotide” refers to a nucleic acid molecule that encodes a Dj 1 polypeptide. For example, SEQ ID NOs: 2 and 5 are nucleic acid sequences of Dj 1 polynucleotides, and SEQ ID NOs: 1, 3, and 4 are amino acid sequences of Dj l polypeptides. Thus, the phrase “Dj 1 polypeptide or polynucleotide encoding a Dj 1 polypeptide or fragment thereof’ refers to a Dj 1 polypeptide or a Dj 1 polynucleotide.

By “disease” is meant any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ. Examples of diseases include non-alcoholic fatty liver disease (NAFLD), steatohepatitis, type II diabetes, hyperglycemia, hyperlipidemia, dyslipidemia, obesity, hyperinsulinemia, insulin resistance, hypercholesterolemia, non- familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, atherosclerosis, early onset coronary heart disease, dyslipidemia, hypertriglyceridemia, hyperfattyacidemia, and cirrhosis.

By “effective amount” is meant the amount of a required to ameliorate the symptoms of a disease relative to an untreated patient. The effective amount of active compound(s) used to practice the present invention for therapeutic treatment of a disease varies depending upon the manner of administration, the age, body weight, and general health of the subject. Ultimately, the attending physician or veterinarian will decide the appropriate amount and dosage regimen. Such amount is referred to as an “effective” amount.

By “fragment” is meant a portion of a polypeptide or nucleic acid molecule. This portion contains, preferably, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nucleotides or amino acids.

The terms “isolated,” “purified,” or “biologically pure” refer to material that is free to varying degrees from components which normally accompany it as found in its native state. “Isolate” denotes a degree of separation from original source or surroundings. “Purify” denotes a degree of separation that is higher than isolation. A “purified” or “biologically pure” protein is sufficiently free of other materials such that any impurities do not materially affect the biological properties of the protein or cause other adverse consequences. That is, a nucleic acid or peptide of this invention is purified if it is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Purity and homogeneity are typically determined using analytical chemistry techniques, for example, polyacrylamide gel electrophoresis or high performance liquid chromatography. The term “purified” can denote that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. For a protein that can be subjected to modifications, for example, phosphorylation or glycosylation, different modifications may give rise to different isolated proteins, which can be separately purified.

By “isolated polynucleotide” is meant a nucleic acid (e.g., a DNA) that is free of the genes which, in the naturally-occurring genome of the organism from which the nucleic acid molecule of the invention is derived, flank the gene. The term therefore includes, for example, a recombinant DNA that is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or that exists as a separate molecule (for example, a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. In addition, the term includes an RNA molecule that is transcribed from a DNA molecule, as well as a recombinant DNA that is part of a hybrid gene encoding additional polypeptide sequence.

By an “isolated polypeptide” is meant a polypeptide of the invention that has been separated from components that naturally accompany it. Typically, the polypeptide is isolated when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated. Preferably, the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight, a polypeptide of the invention. An isolated polypeptide of the invention may be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid encoding such a polypeptide; or by chemically synthesizing the protein. Purity can be measured by any appropriate method, for example, column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis. The term “modulate” as used herein includes the inhibition or suppression of a function or activity (such as cell signaling) as well as the enhancement of a function or activity.

The phrase “pharmaceutically acceptable” is art-recognized. In certain embodiments, the term includes compositions, excipients, adjuvants, polymers and other materials and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

By “marker” is meant any protein or polynucleotide having an alteration in expression level or activity that is associated with a disease or disorder.

As used herein, “obtaining” as in “obtaining an agent” includes synthesizing, purchasing, or otherwise acquiring the agent.

By “reduces” is meant a negative alteration of at least 10%, 25%, 50%, 75%, or 100%.

By “reference” is meant a standard or control condition.

A “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset of or the entirety of a specified sequence; for example, a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence. For polypeptides, the length of the reference polypeptide sequence will generally be at least about 16 amino acids, preferably at least about 20 amino acids, more preferably at least about 25 amino acids, and even more preferably about 35 amino acids, about 50 amino acids, or about 100 amino acids. For nucleic acids, the length of the reference nucleic acid sequence will generally be at least about 50 nucleotides, preferably at least about 60 nucleotides, more preferably at least about 75 nucleotides, and even more preferably about 100 nucleotides or about 300 nucleotides or any integer thereabout or therebetween.

Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity. Polynucleotides having “substantial identity” to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity. Polynucleotides having “substantial identity” to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. By “hybridize” is meant pair to form a double-stranded molecule between complementary polynucleotide sequences (e.g., a gene described herein), or portions thereof, under various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399; Kimmel, A. R. (1987) Methods Enzymol. 152:507).

For example, stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate, preferably less than about 500 mM NaCl and 50 mM trisodium citrate, and more preferably less than about 250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, while high stringency hybridization can be obtained in the presence of at least about 35% formamide, and more preferably at least about 50% formamide. Stringent temperature conditions will ordinarily include temperatures of at least about 30° C, more preferably of at least about 37° C, and most preferably of at least about 42° C. Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion of carrier DNA, are well known to those skilled in the art. Various levels of stringency are accomplished by combining these various conditions as needed. In a preferred: embodiment, hybridization will occur at 30° C in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. In a more preferred embodiment, hybridization will occur at 37° C in 500 mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and 100 pg/ml denatured salmon sperm DNA (ssDNA). In a most preferred embodiment, hybridization will occur at 42° C in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and 200 pg/ml ssDNA. Useful variations on these conditions will be readily apparent to those skilled in the art.

For most applications, washing steps that follow hybridization will also vary in stringency. Wash stringency conditions can be defined by salt concentration and by temperature. As above, wash stringency can be increased by decreasing salt concentration or by increasing temperature. For example, stringent salt concentration for the wash steps will preferably be less than about 30 mM NaCl and 3 mM trisodium citrate, and most preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate. Stringent temperature conditions for the wash steps will ordinarily include a temperature of at least about 25° C, more preferably of at least about 42° C, and even more preferably of at least about 68° C. In a preferred embodiment, wash steps will occur at 25° C in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, wash steps will occur at 42 C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, wash steps will occur at 68° C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additional variations on these conditions will be readily apparent to those skilled in the art. Hybridization techniques are well known to those skilled in the art and are described, for example, in Benton and Davis (Science 196: 180, 1977); Grunstein and Hogness (Proc. Natl. Acad. Sci., USA 72:3961, 1975); Ausubel et al. (Current Protocols in Molecular Biology, Wiley Interscience, New York, 2001); Berger and Kimmel (Guide to Molecular Cloning Techniques, 1987, Academic Press, New York); and Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York.

By “substantially identical” is meant a polypeptide or nucleic acid molecule exhibiting at least 50% identity to a reference amino acid sequence (for example, any one of the amino acid sequences described herein) or nucleic acid sequence (for example, any one of the nucleic acid sequences described herein). Preferably, such a sequence is at least 60%, more preferably 80% or 85%, and more preferably 90%, 95% or even 99% identical at the amino acid level or nucleic acid to the sequence used for comparison.

Sequence identity is typically measured using sequence analysis software (for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705, BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and/or other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. In an exemplary approach to determining the degree of identity, a BLAST program may be used, with a probability score between e'³ and e'¹⁰⁰ indicating a closely related sequence.

By “subject” is meant a mammal, including, but not limited to, a human or nonhuman mammal, such as a bovine, equine, canine, ovine, or feline.

Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.

As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disease, disorder, condition, and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disease, disorder, or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.

As used herein, a therapeutic that “prevents” a disorder or condition refers to a compound that, in a statistical sample, reduces the occurrence of the disorder or condition in the treated sample relative to an untreated control sample, or delays the onset or reduces the severity of one or more symptoms of the disorder or condition relative to the untreated control sample.

As used herein, the phrase “conjoint administration” refers to any form of administration of two or more different therapeutic agents such that the second agent is administered while the previously administered therapeutic agent is still effective in the body (e.g., the two agents are simultaneously effective in the patient, which may include synergistic effects of the two agents). For example, the different therapeutic compounds can be administered either in the same formulation or in separate formulations, either concomitantly or sequentially. Thus, an individual who receives such treatment can benefit from a combined effect of different therapeutic agents.

Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive. Unless specifically stated or obvious from context, as used herein, the terms “a,” “an,” and “the” are understood to be singular or plural.

Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about.

Protein Deglycase DJ-1 (Djl)

Dj 1 (encoded by Park7 gene) is a small and highly conserved protein of 189 amino acids. Mutations in Dj 1 cause autosomal recessive forms of Parkinson’s disease (PD), and the protein has been implicated in various cellular processes, including homeostatic control of reactive oxygen species (ROS), transcription regulation, protein folding, modulation of glucose levels, fertility, and cellular transformation (3). Representative human nucleic and amino acid sequences of Dj l are provided below.

Human Dj 1 amino acid sequence (SEQ ID NO: 1):

>NP 001116849 . 1 Parkinson disease protein 7 [ Homo sapiens]

1 mas kralvil akgaeemetv ipvdvmrrag ikvtvaglag kdpvqcs rdv vicpdasled

61 akkegpydvv vlpggnlgaq nlsesaavke ilkeqenrkg liaaicagpt allaheigf g

121 s kvtthplak dkmmngghyt ysenrvekdg lilts rgpgt s fefalaive alngkevaaq

181 vkaplvlkd

Human Dj 1 nucleic acid sequence (mRNA, CDS 49-618) (SEQ ID NO: 2)

>NM 001123377 . 2 Homo sapiens Parkinsonism as sociated deglycase ( PARK7 ) , trans cript variant 2 , mRNA

1 gcgttcattt tcagcctggt gtggggcttg taaacatata acataaaaat ggcttccaaa

61 agagctctgg tcatcctggc taaaggagca gaggaaatgg agacggtcat ccctgtagat 121 gtcatgaggc gagctgggat taaggtcacc gttgcaggcc tggctggaaa agacccagta 181 cagtgtagcc gtgatgtggt catttgtcct gatgccagcc ttgaagatgc aaaaaaagag 241 ggaccatatg atgtggtggt tctaccagga ggtaatctgg gcgcacagaa tttatctgag 301 tctgctgctg tgaaggagat actgaaggag caggaaaacc ggaagggcct gatagccgcc 361 atctgtgcag gtcctactgc tctgttggct catgaaatag gttttggaag taaagttaca 421 acacaccctc ttgctaaaga caaaatgatg aatggaggtc attacaccta ctctgagaat 481 cgtgtggaaa aagacggcct gattcttaca agccgggggc ctgggaccag cttcgagttt 541 gcgcttgcaa ttgttgaagc cctgaatggc aaggaggtgg cggctcaagt gaaggctcca 601 cttgttctta aagactagag cagcgaactg cgacgatcac ttagagaaac aggccgttag 661 gaatccattc tcactgtgtt cgctctaaac aaaacagtgg taggttaatg tgttcagaag 721 tcgctgtcct tactactttt gcggaagtat ggaagtcaca actacacaga gatttctcag 781 cctacaaatt gtgtctatac atttctaagc cttgtttgca gaataaacag ggcatttagc 841 aaactactga ttgtttcttg ttttgtctct catttctttt gtgaaattaa attccgtatc 901 accttcattt gcagctctta actgtccata tggcactgaa ataaaagaac agtgaccaca 961 ttttacacag caaggaggaa aggcatacaa acagaattta agaggcttgt gattttctct 1021 gcttattagc tgtgtgtttt taatgtgcta ttaaaaaata ccaatgagg

Mouse (We only tested tDj 1 in mouse models) tDj 1 amino acid sequence (SEQ ID NO: 3):

32 kvtvaglag kdpvqcs rdv micpdtsled

61 aktqgpydvv vlpggnlgaq nlsespmvke ilkeqes rkg liaaicagpt allahevgfg 121 ckvtthplak dkmmngshys yses rvekdg lilts rgpgt s fefalaive

Mouse Dj 1 Amino Acid Sequence (SEQ ID NO:4)

>NP 065594 . 2 Parkinson disease protein 7 homolog [Mus muscul us]

1 mas kralvil akgaeemetv ipvdvmrrag ikvtvaglag kdpvqcs rdv micpdtsled

61 aktqgpydvv vlpggnlgaq nlsespmvke ilkeqes rkg liaaicagpt allahevgfg

121 ckvtthplak dkmmngshys yses rvekdg lilts rgpgt s fefalaive alvgkdmanq 181 vkaplvlkd Mouse Dj 1 nucleic acid sequence (mRNA, CDS 156-725) (SEQ ID NO: 5)

>NM 020569 . 3 Mus muscul us Parkinson disease ( autosomal reces sive , early onset ) 7 ( Park7 ) , mRNA

1 tgacgcaggc cgaggcggaa gcgaggggtt gtgcgcagcc tcagtgcggg tggcgcgcat

61 gcgtgctggg tacacgtcgg gtgcgaggtt cctgcggact agcggtggct tcgcgtgggt 121 ggaggaggcg cggctgcagt ctttaagaaa tagaaatggc ttccaaaaga gctctggtca 181 tcctggccaa aggagcagag gagatggaga cagtgattcc tgtggatgtc atgcggcgag 241 ccgggatcaa agtcactgtt gcaggcttgg ctgggaagga ccccgtgcag tgtagccgtg 301 atgtaatgat ttgtccagat accagtctgg aagatgcaaa aacgcaggga ccatacgatg 361 tggtggttct tccaggagga aatctgggtg cacagaattt atctgagtcg cctatggtga 421 aggagatcct caaggagcag gagagcagga agggcctcat agctgccatc tgtgcaggtc 481 ctacggctct gttggctcac gaagtaggtt ttggatgcaa ggtcacaaca cacccactgg 541 ctaaggacaa aatgatgaat ggcagtcact acagctactc agagagccgc gtggagaagg 601 acggcctgat cctcaccagc cgcgggccgg ggaccagctt tgagtttgca ctagccattg 661 tggaggcact cgtggggaaa gacatggcca accaagtgaa ggcaccgctt gttctcaaag 721 actagagccc aagccctggg ccccacgctt gagcaggcat tggaagccca ctggtgtgtc 781 cagagcccag ggaacctcag cagtagtatg tgaagcagcc gccacacggg gctctcatcc 841 cgggtctgta tgtttctgaa ccttgctagt agaataaaca gtttaccaag ctcctgccag 901 ctaaaaaaaa aaaaaaaaaa

It is widely accepted that Dj 1 protects neuronal cells by directly quenching reactive oxygen species (ROS) upon oxidative modification of a conserved cysteine residue and promotes efficient fuel utilization in other organs such as skeletal muscle (4). Moreover, numerous studies have found that Dj 1 level was elevated in the body fluid such as plasma, urine, and cerebrospinal fluid in Parkinson’s disease (PD) patients (5-11). However, the molecular mechanisms underlying circulating Dj 1 function remain unclear. This disclosure provides novel compositions and methods based on the discoveries presented herein related to Dj 1 expression and function.

For example, nucleic acid molecules encompassed by the present invention encode a Dj 1 polypeptide or a fragment thereof. If the polynucleotide is a fragment of the full-length coding sequence of a Dj 1 polypeptide, then the polynucleotide encodes a biologically active fragment of a Dj 1 polypeptide. Such Dj 1 polynucleotides have a nucleotide sequence that is at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95% or more (e.g., about 98%) homologous to the nucleotide sequence shown in SEQ ID NO: 2 or 5 or a portion thereof (i.e., 100, 200, 300, 400, 450, 500, or more nucleotides). Such polynucleotides may be isolated using standard molecular biology techniques and the sequence information provided herein. Alternatively, such polynucleotides may be isolated by polymerase chain reaction using oligonucleotide primers designed based upon the sequence of SEQ ID NO: 2 or 5, or fragment thereof, or the homologous nucleotide sequence. For example, mRNA may be isolated from cells (i.e., by the guanidinium- thiocyanate extraction procedure of Chirgwin el al. (1979) Biochemistry 18: 5294-5299) and cDNA may be prepared using reverse transcriptase (i.e., Moloney MLV reverse transcriptase, available from Gibco/BRL, Bethesda, MD; or AMV reverse transcriptase, available from Seikagaku America, Inc., St. Petersburg, FL). Synthetic oligonucleotide primers for PCR amplification may be designed based upon the nucleotide sequence of SEQ ID NO: 2 or 5, or fragment thereof, or to a homologous nucleotide sequence. A nucleic acid encompassed by the present invention can be amplified using cDNA or, alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. Furthermore, oligonucleotides corresponding to a Dj 1 nucleotide sequence may be prepared by standard synthetic techniques, i.e., using an automated DNA synthesizer.

Nucleic acid molecules encoding other Dj 1 members that have a nucleotide sequence differing from SEQ ID NO: 2 or 5, or fragment thereof, are contemplated. Moreover, nucleic acid molecules encoding Dj 1 proteins from different species (e.g., mouse), and thus have a nucleotide sequence that differs from the Dj 1 sequence of SEQ ID NO: 2 or 5, are also intended to be within the scope of the present invention.

In certain embodiments, nucleic acid molecule(s) encompassed by the present invention encode a protein or portion thereof that includes an amino acid sequence sufficiently homologous to an amino acid sequence of SEQ ID NO: 1, 3, or 4, or fragment thereof, such that the protein or portion thereof increases fatty acid oxidation and decreases lipid content in the liver by improving mitochondrial activity, suppresses ASKl-JNK-PPARa signaling in the liver, improves glucose homeostasis in non-alcoholic steatohepatitis (NASH) mice, reduces inflammation and cell apoptosis in the liver, and ameliorates liver fibrosis.

As used herein, the language “sufficiently homologous” refers to proteins or portions thereof that have amino acid sequences that include a minimum number of identical or equivalent amino acid residues (e.g., an amino acid residue that has a similar side chain as an amino acid residue in SEQ ID NO: 1, 3, or 4, or fragment thereof) to an amino acid sequence of SEQ ID NO: 1, 3, or 4, or fragment thereof, such that the protein or portion thereof, once administered to a subject 1) increases fatty acid oxidation; 2) decreases lipid content in the liver; 3) suppresses ASKl-JNK-PPARa signaling in the liver; 4) improves glucose homeostasis in non-alcoholic steatohepatitis (NASH) mice; and 5) reduces inflammation, cell apoptosis, and fibrosis in the liver. The Dj 1 protein, or fragment thereof, can be at least about 50%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more homologous to the entire amino acid sequence of SEQ ID NO: 1, 3, or 4 or fragment thereof. The proteins of the present invention have at least one biologically active portion. As used herein, the term “biologically active portion” is intended to include a portion, e.g., a domain/motif, of Dj 1 that has one or more of the biological activities of the full-length Dj 1 protein, such as listed above.

The polynucleotides and polypeptides described herein can be isolated or purified using methods well known in the art. The Dj 1 polynucleotides and polypeptides can be recombinant nucleic acid molecules or polypeptides. Dj 1 polynucleotides can be DNA or RNA. In some embodiments, the Dj 1 polynucleotides are incorporated into a vector (e.g., a cloning or expression vector).

Dj 1 agonists are also contemplated herein. Relevant agonists increase the expression or activity of a Dj 1 polynucleotide or polypeptide. An agonist may directly increase the expression or activity of a Dj 1 polynucleotide or polypeptide or the agonist may act indirectly. For example, an agonist may act indirectly to increase the expression or activity of a Dj 1 polynucleotide or polypeptide by promoting the activity or expression of a polynucleotide or polypeptide that acts to increase the expression or activity of a Dj 1 polynucleotide or polypeptide. Alternatively, a Dj 1 agonist may act indirectly by inhibiting the expression of activity of a polynucleotide or polypeptide that, when expressed, inhibits, impairs, or otherwise downregulates the expression or activity of a Dj 1 polynucleotide or polypeptide. For example, an inhibitory nucleic acid (e.g., an siRNA) can inhibit expression of activity of a polynucleotide that, when expressed, inhibits, impairs, or otherwise downregulates the expression or activity of a Dj 1 polynucleotide or polypeptide. Dj 1 agonists are known in the art (e.g., sodium phenylbutyrate and D2R) have been shown to upregulate the expression or activity of Dj 1 (53).

Pharmaceutical Compositions

The compositions and methods of the present invention may be utilized to treat an individual in need thereof. In certain embodiments, the individual is a mammal such as a human, or a non-human mammal. When administered to an animal, such as a human, the composition, nucleic acid, or protein is preferably administered as a pharmaceutical composition comprising, for example, a protein of the invention and a pharmaceutically acceptable carrier. A composition can comprise, for example, a Dj 1 polypeptide or a fragment thereof or a polynucleotide encoding a Dj 1 polypeptide or a fragment thereof and a pharmaceutically acceptable carrier.

Pharmaceutically acceptable carriers are well known in the art and include, for example, aqueous solutions such as water or physiologically buffered saline or other solvents or vehicles such as glycols, glycerol, oils such as olive oil, or injectable organic esters. In preferred embodiments, when such pharmaceutical compositions are for human administration, particularly for invasive routes of administration (z.e., routes, such as injection that circumvents transport or diffusion through an epithelial barrier), the aqueous solution is pyrogen-free, or substantially pyrogen-free. The excipients can be chosen, for example, to effect delayed release of an agent or to selectively target one or more cells, tissues, or organs. The pharmaceutical composition can be in dosage unit form such as tablet, capsule (including sprinkle capsule and gelatin capsule), granule, lyophile for reconstitution, powder, solution, syrup, suppository, injection or the like. The composition can also be present in a transdermal delivery system, e.g., a skin patch. The composition can also be present in a solution suitable for topical administration, such as a lotion, cream, or ointment.

The phrase “pharmaceutically acceptable carrier” as used herein means a pharmaceutically acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient. Some examples of materials which can serve as pharmaceutically acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) phosphate buffer solutions; and (21) other non-toxic compatible substances employed in pharmaceutical formulations. A pharmaceutically acceptable carrier can contain physiologically acceptable agents that act, for example, to stabilize, increase solubility or to increase the absorption of a compound such as tofacitinib. Such physiologically acceptable agents include, for example, carbohydrates, such as glucose, sucrose or dextrans, antioxidants, such as ascorbic acid or glutathione, chelating agents, low molecular weight proteins or other stabilizers or excipients. The choice of a pharmaceutically acceptable carrier, including a physiologically acceptable agent, depends, for example, on the route of administration of the composition. The preparation or pharmaceutical composition can be a self-emulsifying drug delivery system or a self-microemulsifying drug delivery system. The pharmaceutical composition (preparation) also can be a liposome or other polymer matrix, which can have incorporated therein, for example, a compound of the invention. Liposomes, for example, which comprise phospholipids or other lipids, are nontoxic, physiologically acceptable and metabolizable carriers that are relatively simple to make and administer.

The phrase “pharmaceutically acceptable” is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

A pharmaceutical composition (preparation) can be administered to a subject by any of a number of routes of administration including, for example, orally (for example, drenches as in aqueous or non-aqueous solutions or suspensions, tablets, capsules (including sprinkle capsules and gelatin capsules), boluses, powders, granules, pastes for application to the tongue); absorption through the oral mucosa (e.g., sublingually); subcutaneously; transdermally (for example as a patch applied to the skin); and topically (for example, as a cream, ointment or spray applied to the skin). The compound may also be formulated for inhalation. In certain embodiments, a compound may be simply dissolved or suspended in sterile water. Details of appropriate routes of administration and compositions suitable for same can be found in, for example, U.S. Pat. Nos. 6,110,973, 5,763,493, 5,731,000, 5,541,231, 5,427,798, 5,358,970 and 4,172,896, as well as in patents cited therein.

The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, the particular mode of administration. The amount of active ingredient that can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound that produces a therapeutic effect. Generally, out of one hundred percent, this amount will range from about 1 percent to about ninety-nine percent of active ingredient, preferably from about 5 percent to about 70 percent, most preferably from about 10 percent to about 30 percent.

Methods of preparing these formulations or compositions include the step of bringing into association an active Dj 1 protein or fragment thereof or nucleic acid encoding such protein or fragment thereof with the carrier and, optionally, one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association a compound of the present invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.

Formulations of the invention suitable for oral administration may be in the form of capsules (including sprinkle capsules and gelatin capsules), cachets, pills, tablets, lozenges (using a flavored basis, usually sucrose and acacia or tragacanth), lyophile, powders, granules, or as a solution or a suspension in an aqueous or non-aqueous liquid, or as an oil-in- water or water-in-oil liquid emulsion, or as an elixir or syrup, or as pastilles (using an inert base, such as gelatin and glycerin, or sucrose and acacia) and/or as mouth washes and the like, each containing a predetermined amount of a compound of the present invention as an active ingredient. Compositions or compounds may also be administered as a bolus, electuary, or paste.

To prepare solid dosage forms for oral administration (capsules (including sprinkle capsules and gelatin capsules), tablets, pills, dragees, powders, granules and the like), the active ingredient is mixed with one or more pharmaceutically acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose and/or acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as, for example, cetyl alcohol and glycerol monostearate; (8) absorbents, such as kaolin and bentonite clay; (9) lubricants, such a talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof; (10) complexing agents, such as, modified and unmodified cyclodextrins; and (11) coloring agents. In the case of capsules (including sprinkle capsules and gelatin capsules), tablets and pills, the pharmaceutical compositions may also comprise buffering agents. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like.

A tablet may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared using binder (for example, gelatin or hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (for example, sodium starch glycolate or cross-linked sodium carboxymethyl cellulose), surface-active or dispersing agent. Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.

The tablets, and other solid dosage forms of pharmaceutical compositions, such as dragees, capsules (including sprinkle capsules and gelatin capsules), pills and granules, may optionally be scored or prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical-formulating art. They may also be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile, other polymer matrices, liposomes and/or microspheres. They may be sterilized by, for example, filtration through a bacteria-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions that can be dissolved in sterile water, or some other sterile injectable medium immediately before use. These compositions may also optionally contain opacifying agents and may be of a composition that they release the active ingredient(s) only, or preferentially, in a certain portion of the gastrointestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes. The active ingredient can also be in micro- encapsulated form, if appropriate, with one or more of the above-described excipients.

Liquid dosage forms useful for oral administration include pharmaceutically acceptable emulsions, lyophiles for reconstitution, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredient, the liquid dosage forms may contain inert diluents commonly used in the art, such as, for example, water or other solvents, cyclodextrins and derivatives thereof, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.

Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming and preservative agents.

Suspensions, in addition to the active compounds, may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.

As used herein, the term “administering” a substance, such as a therapeutic entity to an animal or cell” is intended to refer to dispensing, delivering or applying the substance to the intended target. In terms of the therapeutic agent, the term “administering” is intended to refer to contacting or dispensing, delivering or applying the therapeutic agent to an animal by any suitable route for delivery of the therapeutic agent to the desired location in the animal, including delivery by oral, transdermal or parenteral administration. Administration by injection can include without limitation, intravenous, intramuscular, intraarterial, intradermal, intraperitoneal, subcutaneous, injection and infusion. Pharmaceutical compositions suitable for parenteral administration comprise one or more active compounds in combination with one or more pharmaceutically acceptable sterile isotonic aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain antioxidants, buffers, bacteriostats, solutes which render the formulation isotonic with the blood of the intended recipient or suspending or thickening agents.

Examples of suitable aqueous and nonaqueous carriers that may be employed in the pharmaceutical compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.

These compositions may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents that delay absorption such as aluminum monostearate and gelatin.

The subject receiving this treatment is any animal in need, including primates, in particular humans, and animal models.

In certain embodiments, compounds of the invention may be used alone or conjointly administered with another type of therapeutic agent.

Methods of Treatment

The present invention provides methods of treating disease and/or disorders or symptoms thereof that comprise administering a therapeutically effective amount of a pharmaceutical composition comprising a Dj 1 protein or fragment thereof or a polynucleotide encoding a Dj 1 polypeptide or a fragment thereof to a subject (e.g., a mammal such as a human). Thus, certain embodiments relate to a method of treating a subject suffering from or susceptible to a disease or disorder or symptom thereof. The method includes the step of administering to the subject a therapeutic amount of a Dj 1 protein or fragment thereof or a polynucleotide encoding a Dj 1 polypeptide or a fragment thereof sufficient to treat the disease or disorder or symptom thereof under conditions such that the disease or disorder is treated.

Identifying a subject in need of such treatment can be in the judgment of a subject or a health care professional and can be subjective (e.g., opinion) or objective (e.g., measurable by a test or diagnostic method).

The administration of a Dj 1 protein or fragment thereof or a polynucleotide encoding a Dj 1 polypeptide or a fragment thereof to a subject increases the expression or activity of a Dj 1 protein. Increased expression or activity of a Dj 1 protein or fragment thereof 1) increases fatty acid oxidation; 2) decreases lipid content in the liver; 3) suppresses the ASK1- JNK signaling in the liver; 4) improves glucose homeostasis in subjects that have nonalcoholic steatohepatitis (NASH); and 5) reduces inflammation, cell apoptosis, and fibrosis in the liver. Subjects having or suspected of having a metabolic disease or disorder, for example, may be characterized by impaired glucose homeostasis, increased lipid content in the liver, and other symptoms, which may be alleviated by administration of a Dj 1 protein or fragment thereof. Examples of metabolic diseases or disorders include, but are not limited to, non-alcoholic fatty liver disease (NAFLD), steatohepatitis, type II diabetes, hyperglycemia, hyperlipidemia, dyslipidemia, obesity, hyperinsulinemia, insulin resistance, hypercholesterolemia, non-familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, atherosclerosis, early onset coronary heart disease, dyslipidemia, hypertriglyceridemia, hyperfattyacidemia, and cirrhosis. Accordingly, the invention generally features methods of increasing or promoting the expression and/or activity of a Dj 1 protein or fragment thereof in a subject having or at risk of developing a metabolic disorder. Therapies provided by the invention include polypeptide therapies and polynucleotide therapies. In one embodiment, the method involves contacting a liver cell of the subject with a Dj 1 protein or fragment thereof or a polynucleotide encoding a Dj 1 polypeptide or a fragment thereof.

In one aspect, methods of treating a metabolic disease or disorder or symptoms thereof are provided that comprise administering a therapeutically effective amount of a pharmaceutical composition comprising an agent described herein that increases expression or activity a Dj 1 protein or fragment thereof to a subject (e.g., a mammal, such as a human). The method includes the step of administering to the mammal a therapeutic amount of an agent described herein sufficient to treat the disease or disorder or symptom thereof under conditions such that the disease, disorder, or symptom is treated.

Another aspect provides a method of reducing fat accumulation in the liver of a subject in which the subject is administered a therapeutically effective amount of a Dj 1 polypeptide or fragment thereof or a polynucleotide encoding a Dj 1 polypeptide or fragment thereof. In some embodiments, the subject being administered a Dj 1 protein or fragment thereof or a polynucleotide encoding a Dj 1 polypeptide or a fragment thereof is also administered a lipid-lowering agent. Examples of lipid lowering agents include atorvastatin, simvastatin, rosuvastatin, fluvastatin, ezetimibe, niacin, bezafibrate, ciprofibrate, clofibrate, gemfibrozil, and fenofibrate.

Dj 1 polypeptides can reduce blood glucose levels and as such represent a novel approach to treating type 2 diabetes. Accordingly, a method is provided for blood glucose levels in which a subject is administered a therapeutically effective amount of a Dj 1 polypeptide or fragment thereof or a polynucleotide encoding a Dj 1 polypeptide or a fragment thereof. This method can further comprise administering to the subject a therapeutically effective amount of insulin, GLP-1, metformin, or a DPP4 inhibitor. In certain embodiments, a Dj 1 agonist may be used instead of, or conjointly with, a Dj 1 polypeptide or polynucleotide in the therapeutic methods described herein.

Such treatments will be suitably administered to subjects, particularly humans, suffering from, having, susceptible to, or at risk for a disease, disorder, or symptom thereof. Administration of the therapeutic agent can be accomplished orally, transdermally, or parenterally. Administration by injection can include without limitation, intravenous, intramuscular, intraarterial, intradermal, intraperitoneal, and subcutaneous injection or infusion.

Diagnostic and Prognostic Methods

As demonstrated herein, Dj 1 can be released from muscle cells, and an increased expression level of Dj 1 in a subject sample relative to a normal control is correlated with a muscle injury. Thus, Dj 1 is a marker for muscle injury. Based on this discovery, methods are provided for detecting the existence of muscle injury, determining susceptibility to muscle injury in a subject, and determining the progression of muscle injury in a subject. Each of these methods comprises detecting or assessing the expression level of Dj 1.

Marker expression can be detected and/or measured at the transcript or protein level by methods well-known in the art. Detecting expressed transcripts (e.g., PARK7 transcripts) in a sample generally involves contacting the sample with a nucleic acid molecule comprising a nucleotide sequence that is at least partially complementary to the nucleic acid sequence of the transcript to be measured under conditions suitable for hybridization. In some embodiments, the nucleic acid molecule is labeled to allow visualization of the molecule after contacting the sample. In some embodiments, the nucleic acid molecule is present on the surface of a substrate. In some embodiments, the substrate comprises a microarray. In some embodiments, the nucleic acid molecule, or a portion thereof, present in a sample is amplified (e.g., by PCR, RT-PCR, etc.), and the amplified product is quantified, thereby providing an estimate of the concentration of the marker in a sample.

Marker expression can also be detected and quantified, in some embodiments, at the protein level. Antibodies that specifically bind a marker, or any other method known in the art, can be used to monitor expression of a marker of interest. Detection of an alteration relative to a normal reference sample can be used as a diagnostic indicator of muscle injury. Similarly, detection of alterations or similarities relative to a reference sample derived from a subject having muscle injury can be used as a diagnostic indicator of muscle injury. The methods described herein can be used to diagnose an individual or to confirm the results of another diagnostic method. Additionally, the methods described herein, or known in the art, can be use used with any other diagnostic method described herein for a more accurate diagnosis of the presence or severity of muscle injury.

In some embodiments, individual markers (i.e., Dj 1) are used in combination with other identified markers, or with other markers known in the art that are associated with muscle injury or treatment thereof. Individual markers, or combinations thereof, are differentially expressed in a subject and, therefore, differentially present in samples from a subject having muscle injury and from a normal subject in whom muscle injury is undetectable. In some embodiments, the Dj 1 protein or polynucleotide level can be compared to a Dj 1 protein or polynucleotide level observed in a control afflicted with the disease, disorder, or condition the subject has or is suspected of having. Thus, levels observed in the subject that are similar or the same as levels observed in an afflicted control are indicative of the subject having the disease, disorder, or condition.

In one aspect, a method is provided for detecting muscle injury in a subject by assessing the level of a Dj 1 polypeptide or polynucleotide, wherein an elevated Dj 1 polypeptide or polynucleotide level relative to a normal control indicates that the subject has muscle injury. In another aspect, a method is provided for determining susceptibility to muscle injury by assessing the level of a Dj 1 polypeptide or polynucleotide, wherein an elevated Dj 1 polypeptide or polynucleotide level relative to a normal control indicates that the subject is susceptible to muscle injury. Thus, elevated Dj 1 levels would be expected in such an individual due to higher basal level of muscle injury than in a subject not predisposed to muscle injury. The progression of muscle injury can also be determined by assessing the level of a Dj 1 polypeptide or polynucleotide, wherein an elevated Dj 1 polypeptide or polynucleotide level relative to a normal control indicates muscle damage progression.

Subjects that have or are susceptible to muscle injury may have a disease or condition that predisposes them to muscle injury. Examples of diseases that could predispose someone to muscle damage include, but are not limited to, amyotrophic lateral sclerosis, Charcot- Marie-Tooth disease, multiple sclerosis, muscular dystrophy, myasthenia gravis, myopathy, myositis, peripheral neuropathy, spinal muscular atrophy, cardiac myopathy, rhabdomyolysis, myasthenia gravis, fibrositis, cramp, and sarcopenia. EXAMPLES

The invention, now being generally described, will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present invention and are not intended to limit the invention.

Example 1 : Materials and Methods

Animals

C57BL/10cSn-Drnd^mdx/J (001801, mdx) and C57BL/10ScSnJ (000476, WT) mice were ordered directly from The Jackson Laboratory. Different ages of mdx and WT mice were obtained. Animals were weaned 21 days after birth and had free access to food and water and were housed on 12 h light-dark cycle. C57BL/6J males were introduced to a normal diet (NC, Research Diets D15100601) or high-fat diet (HFD, Research Diets D 12331), and maintained on a diet for the indicated time. The HFD diet derives 58% of its kilocalories (kcal) from fat (soybean and coconut oil), 25.5% from carbohydrates (sucrose and maltodextrin), and 16.4% from protein (casein). NASH model mice were fed for up to 28 weeks with the NASH diet (Envigo, TD.120528) and 42% fructose (Sigma, F0127) in the water (1,2). The NASH diet is composed of 405.36 g/Kg sucrose and 12.5 g/Kg cholesterol. Recombinant mouse Dj 1 protein (Novus, NBP2-59523) or truncated mouse Dj 1 (tDj 1, GenScript) protein was intravenously injected every day for 5 days or every other day for 2 weeks. Skeletal muscle-specific Park7 knockout mice were generated by crossing Park7 flox mice with Myll-cre mice (J AX, #024713). Mice were raised in microisolator cages with a 12 h : 12 h light : dark cycle. All procedures were performed in accordance with the Guide for Care and Use of Laboratory Animals of the National Institutes of Health, and were approved by the Animal Subjects Committee of the University of California, Los Angeles.

Exercise Training

Acute Endurance Exercise: Experimental groups comprised no running/ sedentary (SED), 45 minutes exercise (EX45), 90 minutes exercise (EX90), and 90 minutes exercise + three-hour rest (EX90 + 3 hr Rest). The moderate-intensity endurance exercise protocol consisted of treadmill running (5% grade) at 15 m/min for the allotted time. This exercise protocol has been shown to represent moderate-intensity exercise in mice (3,4). All mice were acclimated to the treadmill by running for 10 minutes at 5-10 m/min on two separate occasions during the 2-4 days prior to experimentation. Mice in the SED groups were fasted for approximately six hours before tissue harvest. Mice in the EX90 were fasted for approximately three hours prior to exercising. Similarly, all mice were given access to water during the fasting period. Tissues were removed immediately following exercise completion and snap-frozen in liquid nitrogen prior to storage in a -80°C freezer and further analysis.

Endurance exercise training: Experimental groups consisted of: no voluntary wheel running (SED) or 30 days of in cage voluntary wheel running (TRN). All mice were individually housed for three days prior to the introduction of the Respironics® Mini Mitter® (Bend, Oregon) in cage running wheels and were given two days to acclimate to the wheels. Wheels in the cages of SED mice were locked throughout the duration of the experiment. Daily running measurements and weekly body weights were taken for 30 consecutive days. After 30 days, running wheels within TRN cages were locked, and all mice remained within their cages for 24 hours. Following the 24-hour period, mice were fasted for approximately six hours after which tissues were removed immediately and snap-frozen in liquid nitrogen prior to storage in a -80°C freezer and further analysis. Tissue samples were taken approximately 30 hours after locking the running wheels.

Downhill running (DHR): Mice designated for downhill running exercises were first allowed 5 min to ambulate freely on a motorized treadmill set at -10° grade with no belt speed in order to become familiarized with the laboratory environment (5). Following this stationary stage, mice warmed up by running for 6 min at a -22° grade, in which belt speed increased from 5 to 13 m/min. Mice were then given a 3 min rest period before performing a 90-min downhill running protocol that consisted of ten stages at a -22° grade. Each stage began with a 1-min acceleration period (from 5 to 12 m/min), followed by 5 min of constant running at 12 m/min. To prevent exhaustion and ensure that the mice could finish the protocol, each stage was separated by a 2-min rest period. Mice were occasionally prodded with a cotton-tipped applicator to encourage continuous running; the electric shock was prohibited because mice generally responded to a gentle tap on the tail or hindquarters.

Cell culture, reagents, and transfections

Mouse myoblast cells (C2C12) were maintained in high glucose DMEM/high, 10% fetal bovine serum with penicillin/streptomycin. pRK5-Dj 1-HA plasmid was purchased from Addgene (#29396). Seeded cells were cultured in 6-well plates for 24 hours prior to transfection. Transfections were performed using Lipofectamine 2000 and PLUS reagent according to manufacturer instructions (Invitrogen, Carlsbad, CA). Human HepG2 cells were cultured in DMEM/low media containing 10% fetal bovine serum with penicillin/streptomycin. Mouse AML12 cells were maintained in DMEM/F12, ITS supplement (Gibco, USA), 40 ng/ml dexamethasone, and 10% fetal bovine serum with penicillin/streptomycin. For in vitro experiments, HepG2 cells were treated with or without recombinant human Dj 1 protein (Novus, NBC1-18334) in serum-free media containing 25 mM glucose, 200 pM palmitic acid, and 0.25% bovine serum albumin for an indicated time.

Adenovirus Djl

An adenovirus encoding mouse Dj 1 was generated using the ViraPower Adenoviral Expression System (Invitrogen) according to manufacturer instructions. Briefly, the coding sequence of the mouse Dj 1 gene with flanking BP sites was amplified from the Addgene plasmid # 29396 using High Fidelity Pfx50 DNA polymerase (Invitrogen). Entry clones were obtained by recombination of the purified DNA fragment with the pDONR.221 vector using Gateway BP clonase II. Mouse Dj 1 insert was transferred from the entry clones into the pAd/CMV/V5-DEST vector (Invitrogen) using the Gateway LR Clonase II enzyme mix. The recombinant adenoviral purified plasmid was used to generate adenoviral particles according to the manufacturer’s instructions (Invitrogen). Adenoviral titer was determined using the AdenoX Rapid Titer Kit (Clontech).

Histopathology

Cryosections (10-pm thick transverse sections of frozen muscle cut in a cryostat (Leica) at -20°C) were subjected to hematoxylin & eosin (H&E) staining (10, 54). Liver tissues were fixed in phosphate-buffered 10% formalin and embedded in paraffin wax. Sections were cut and stained with H&E.

Mitochondrial DNA

Total DNA was extracted from cells using DNeasy Blood and Tissue kit (Qiagen, Valencia, CA). Expression levels of mtCOs for mtDNA and 18S for nuclear DNA were assessed by real-time qPCR. The ratio of mtDNA (mtCCh) to nuDNA (18 S) was used as an estimate for comparing mtDNA content between the genotypes.

I minimohlot analyses

Mouse tissue and cell samples were pulverized in liquid nitrogen and homogenized in RIPA lysis buffer containing complete EDTA-Free protease (Roche) and Phosphatase Inhibitor Cocktail 2 (Sigma-Aldrich, St. Louis, MO). All lysates were centrifuged, clarified, and resolved by SDS-PAGE. Samples were transferred to PVDF membranes and subsequently probed with the following antibodies for protein and phospho-protein detection: Dj l (R&D systems, AF3668; Abeam, abl l251), LC3B (Novus, Saint Charles, MO), Chop (Cell Signaling Technology, #2895T), Phospho-eIF2a^Ser51 (Cell Signaling Technology, #3398S) and total eIF2a (Cell Signaling Technology, #5324S). Atf6a (Abeam, ab37149), Xbpls (Cell Signaling Technology, #12782), Phospho- JNK^{Thrl83/Tyr185} (Cell Signaling Technology, #9255S), t-JNK (Cell Signaling Technology, #9252S), Phospho-p38 ^{l lll l 80 l yc l 82} (Cell Signaling Technology, #451 IT), t-p38 (Cell Signaling Technology, #8690T), Phospho- ASKl^Ser967 (Cell Signaling Technology, #3764S), t-ASKl (Cell Signaling Technology, #8662S), Phospho-TAKl^Thrl84/187 (Cell Signaling Technology, #4531), t-TAKl (Cell Signaling Technology, #4505), Phospho-AMPK^Thrl72(Cell Signaling Technology, #2535), t- AMPK (Cell Signaling Technology, #5831), Phospho-ACC^Ser79 (Cell Signaling Technology, #3661), t-ACC (Cell Signaling Technology, #3676), Tom20 (Santa Cruz Biotechnology, sc- 136211), Dgatl (Abeam, ab54037), Cptla (Abeam, abl28568), Ppara (Santa Cruz Biotechnology, sc-398394), Atgl (Cell Signaling Technology, #5831), Cd36 (Proteintech, #18836-1-AP), p62 (Cell Signaling Technology, #5114), Phospho-FoxOl (Cell Signaling Technology, #84192), t-FoxOl (Cell Signaling Technology, #2880), Cleaved-CASP3 (Cell Signaling Technology, #9661), Cleaved-CASP8 (Cell Signaling Technology, #8592), Cleaved-CAPS9 (Cell Signaling Technology, #20750), PARP (Cell Signaling Technology, #9532), c-Flip (Cell Signaling Technology, #56343), a-SMA (Santa Cruz Biotechnology, sc- 53142), b-Actin (Santa Cruz Biotechnology, sc-47778), GAPDH (ThermoFisher Scientific, #PAl-987). Densitometric analyses were performed using BioRad Quantity One image software (Bio-Rad, Hercules, CA).

ELISA

Mouse serum Dj 1 and CK were measured by mouse Park7/DJ-l DuoSet ELISA (DY8136, R&D systems) and mouse CKMB/Creatine Kinase MB ELISA Kit (LS-F5745, LSBio) respectively. Mouse Serum AST and ALT were measured by AST activity assay kit (Sigma, MAK055) and ALT activity assay kit (Sigma, MAK052) respectively.

NEFA, Cholesterol, and Triglyceride assay

Plasma and liver NEFA, Cholesterol, and Triglyceride were analyzed by their respective kits (FUJIFILM Wako Diagnostics)

Liver lipids extraction

About 80 mg of liver samples were homogenized and sonicated in PBS (pH 7.4) for lipid extraction. An internal standard mixture (ISTD) and CHC13 : methanol (2: 1) were added to the samples before being vortexed, mixed, sonicated, and centrifuged. The supernatant containing the lipid was removed and dried, the lipids were resuspended in ethanol and then sonicated.

Plasma be ta-Hydr oxybutyr ate

Plasma beta-Hydroxybutyrate was measured by Cayman beta-Hydroxybutyrate (Ketone Body) Colorimetric Assay kit (Cayman, 700190).

Mouse plasma mass spectrometry

Mouse plasma samples were subject to immunoaffinity removal of 7 highly abundant proteins using Seppro Mouse Spin Columns prior to protein digestion with trypsin. Thermo Scientific TMTIOplex Isobaric Mass Tag Labeling Reagents were utilized to provide multiplex relative quantitation. Peptides were fractionated via high pH reversed-phase chromatography then injected onto a laser-pulled nanopore C18 column with 1.8 pm beads and resolved using a 3-hour gradient optimized on a hybrid quadrupol e-Orbitrap mass spectrometer in dd-MS2 mode. The raw data were analyzed in Proteome Discoverer 2.2, which provided measurements of abundance for the identified peptides.

Intravital imaging of Djl

Recombinant mouse Dj 1 protein (NBP2-59523, Novus) were labeled with nearinfrared dyes using IRDye 800CW protein labeling kit-Low MW (Li-COR Biosciences) as described in the manufacturer’s instructions. 10 pg of labeled Dj 1 protein was injected into wild-type C57BL/6J mouse through the tail vein. The mice were imaged at the indicated time using an IVIS Spectrum (PerkinElmer). For tissue analysis, recipient mice were euthanized by cervical dislocation, and tissues were then dissected and imaged. Fluorescence was detected using excitation and emission filters at 745 nm and 800 nm, respectively.

Live-cell imaging.

C2C12 cells were plated in CELLview 4-compartment glass-bottom tissue culture dishes (Greiner Bio-One, 627870), PS, 35/10 mm. CellMask Plasma Membrane Stains (Cl 0046, Invitrogen) 100 nM 10-A-nonyl acridine orange, 15 nM TMRE, 5 pM Rhol23, and/or 200 nM MitoTracker Green; Invitrogen) were mixed with cell culture media and incubated with GFP -tagged Dj 1 transfected cells 1-3 hrs prior to live-cell imaging with an alpha Plan-Apochromat 100X/1.46 Oil DIC M27 objective on a Zeiss LSM 880 with Airyscan. Before image analysis, raw .czi files were automatically processed into deconvoluted Airyscan images using Zen software. Time-lapse images were acquired at approximately 1 frame/second.

Statistics

Values presented are expressed as means ± SEM. Statistical analyses performed using Student’s /-test when comparing two groups of samples or one-way analysis of variance (ANOVA) with Tukey’s post hoc comparison for identification of significance within and between groups using PASW Statistics 18 statistical software or GraphPad Prism 9. Two-way ANOVA was used for comparisons between mice that were grouped based on genotype. Three-way mixed ANOVA was used to determine group differences over time. Two-tailed independent and dependent Student’s t-tests were also used when appropriate. Significance is set a priori atP < 0.05.

Example 2: Skeletal muscle releases Djl

Dj 1 protein has been detected in the plasma, urine, and cerebrospinal fluid of PD patients (6) and some cancer patients (7). Here, Dj 1 protein was also detected in the culture medium of both primary mouse myotubes and C2C12 myotubes (immortalized mouse muscle cells) (Figure IF). Following treatment with 5 or lOpl of adenovirus-Dj 1, Dj 1 levels in the culture medium of C2C12 myocytes were elevated while cellular Dj 1 levels remained unchanged, suggesting that muscle cells release excess Dj 1 protein (Figure 1G). To further validate muscle cell releases of Dj 1, Dj 1 was overexpressed in C2C12 myocytes by transient transfection of HA-tagged Dj l, resulting in detection of both endogenous Dj 1 and HA-tagged Dj 1 in the culture medium. Interestingly, mitochondrial depolarizer CCCP treatment elevated HA-Dj 1 levels in the media, but did not alter the protein level of cleaved caspase 3, indicating the muscle cell releases of Dj 1 was not due to apoptosis (Figures 1H, II).

To verify that skeletal muscle release of Dj 1 in vivo, the basal plasma Dj 1 levels in male wild-type C57BL/6J mice were determined where levels were slightly increased from 20 ng/ml to 40 ng/ml in 2 to 20 weeks old mice (Figure 1 J). Physical exercise is known to induce the secretion of many myokines. To determine whether exercise stimulates skeletal muscle release of Dj 1, plasma Dj 1 levels were examined in the mice following acute treadmill and chronic running wheel training. It was found that exercise training did not alter plasma Dj 1 levels (Figure IK).

Since CCCP administration elevated Dj l levels in the media of C2C12 myotubes, it was hypothesized that muscle injury or stress may trigger skeletal muscle release of Dj 1. In order to further explore this, plasma Dj 1 levels were examined in three different muscle injury mouse models - dystrophin deletion mdx mice, downhill running mice, and a myotoxin injury mice.

The mdx mouse is a commonly used model to study Duchenne muscular dystrophy (DMD), the most common and severe muscular dystrophy (8). mdx skeletal muscles exhibit active myofiber necrosis (9), and enter a phase of florid myonecrosis at 3 weeks (10). To exclude the impact of myofiber necrosis on protein release, the plasma Dj 1 level of 2 and 4 wk old mdx mice were determined. Surprisingly, both 2 and 4 weeks old mdx mice have strikingly increased circulating Dj 1 levels with unchanged protein levels of Dj 1 in skeletal muscle. In contrast, the plasma CKMB level, an indirect marker of muscle damage, was only elevated in 4 weeks old mdx mice (Figures 1 A, IB, IL, and IM). These results indicate that the plasma Dj 1 levels could be a potential early diagnostic biomarker of muscle dystrophy.

Unaccustomed downhill running is known to induce muscle damage (11). After 90 minutes of downhill running, the mice had significantly increased plasma Dj 1 levels when compared to the sedentary group (SED) (Figures 1C).

Cardiotoxin (CTX) induces skeletal muscle injury and regeneration. To further validate the effect of muscle injury on circulating Dj 1, C57BL/6J mice were injected intramuscularly with CTX, and plasma Dj 1 levels were measured 2 days post-administration. Consistently, an increase of Dj lin the plasma was observed in CTX-treated mice (Figures ID- IE, IN, and 10).

Moreover, plasma Dj 1 levels were significantly reduced in the skeletal musclespecific Park7 knockout mice (mPark7^K0) (> 2 folds down) (Figures IP- IQ), suggesting that skeletal muscle is a primary source of circulating Dj 1. Ultimately, both in vitro and in vivo results indicate that skeletal muscles release Dj 1.

Example 3: Endoplasmic reticulum (ER) stress induces muscle cells release of Djl

Strenuous exercise increases the endoplasmic reticulum (ER) stress, which at an excessive level can lead to muscle damage (12). Accumulating evidence suggests that ER stress is involved in myokine induction (13). To determine the mechanisms that drive skeletal muscle releases of Dj 1, ER stress markers were examined in skeletal muscles of the three different mouse models described above. Consistently, muscles were found to have significantly elevated the protein levels or gene expression of ER stress markers Chop and Atf6a in all three mouse models (Figures 2A-2D), indicating that ER stress might be a trigger of skeletal muscle release of Dj 1. To further validate muscle cells release of Dj 1, in vitro studies were assessed. Indeed, both in vitro and ex vivo studies confirmed that muscle cells release Dj 1 after being treated with the ER stress inducer Thapsigargin (Tg) as well as CCCP (Figures 2E, 2F, and 2L).

Extracellular vesicles are cell-derived membranous structures including exosomes and microvesicles bodies, which are enriched with proteins, lipids, DNA, and RNA (14). To examine whether Dj 1 is released through the extracellular vesicle system, Dj 1 levels were determined in the culture media of C2C12 myotubes that were treated with or without CCCP, Tg, exosome generation inhibitor GW4869, or exocytosis inhibitor Exol. Both GW4869 and Exol treatment significantly reduced the protein level of Dj 1 in the media, indicating that muscle cells release Dj 1 in extracellular vesicles (Figure 2G-2H). To visualize the release of Dj 1 from muscle cells, time-lapse imaging was performed on C2C12 myocytes transfected with Dj 1-GFP. Robust budding of vesicles from C2C12 myocytes treated with Tg or CCCP was observed (Figure 21). Based upon the release pattern and the average 1 pm diameter of budding vesicles, it was hypothesized that Dj 1 was released in shedding microvesicles. To further determine which types of extracellular vesicles were enriched with Dj 1, microvesicle bodies (MVBs) and exosomes from C2C12 culture media and CTX-treated mouse plasma were separated by differential centrifugation. Dj 1 was detected in both MVBs and exosomes of the culture medium and mouse plasma (Figures 2J, 2K). Altogether, these findings showed that ER stress-activated skeletal muscle cells to release Dj 1 in extracellular vesicles.

Example 4: Recombinant Djl protein primarily targets the liver

Myokines contribute to whole-body metabolism by directly signaling to distant organs (15-18). To determine which organs Dj 1 targets, WT mice were tail-vein injected with a recombinant Dj 1 (rDj 1) protein labeled with the near-infrared fluorescent dye IRDye 800CW, and the fluorescent signals were tracked using an optical imaging system (Figures 31, 3 J). A robust fluorescent signal could be detected within 5 minutes post-injection. And most signals were accumulated in the liver, kidney, and urine at 4 hours post-injection (Figures 3A-3C, 3K). Considering that the reagents injected through tail-vein often nonspecifically target the liver, fluorescent-labeled rDj 1 was used to determine whether Dj 1 could bind to the plasma membrane of liver cells. rDj 1 was labeled with Alex 488 and added into the medium of mouse liver cells (AML12 cells) at the indicated time. Fluorescent microscopy detected that rDj 1 colocalized with the plasma membrane of AML12 cells (Figure 3D). Furthermore, rDj 1 treatment elevated the phosphorylation of AMPK and ACC and enhanced the oxygen consumption rate/extracellular acidification rate (OCR/ECAR) and mitochondrial ATP production rate in human liver carcinoma HepG2 cells (Figures 3E-3G and 3L-3N), indicating that rDj 1 enhanced mitochondrial oxidative phosphorylation. RNA sequencing analysis further confirmed upregulated AMPK signaling in rDj 1 -treated HepG2 cells (Figure 3H). These results indicate that rDj 1 primarily targets hepatocytes and activates AMPK signaling and mitochondrial activity.

Example 5: rDjl administration suppresses high-fat diet feeding induced hepatic steatosis

AMPK signaling is vital for lipid metabolism in the liver (19). It was determined that rDj 1 significantly promoted fatty acid oxidation which may contribute to the reduced triacylglycerol (TG) levels and Oil Red O staining (stain neutral lipids) in HepG2 cells (Figures 4A-4C). These findings indicate that Dj 1 could enhance lipid metabolism and ameliorate HFD-induced hepatic steatosis. rDj 1 was tail-vein injected into mice fed with a chow diet (NC) or high-fat diet (HFD) daily for 5 days. Surprisingly, rDj 1 administration significantly reduced plasma non-esterified fatty acids (NEFA) and cholesterol levels in NC- fed mice, while decreasing TGs levels in the liver of HFD-fed mice (Figures 4D-4I). Consistently, liver H&E staining displayed fewer lipids in rDj 1 -treated HFD-fed mice (Figures 4J and 4T). Although body weights and fasting blood glucose levels of HFD-fed mice were unchanged during the rDj 1 administration, rDj 1 indeed enhanced glucose homeostasis and insulin action, as evidenced by improving glucose tolerance tests and insulin tolerance tests, respectively (Figures 4K-4M, 4U-4Z).

Elevated AMPK signaling and reduced lipid content in the liver led to the hypothesis that rDj 1 might activate the whole-body energy metabolism of mouse. Therefore, the metabolic rate was determined in HFD-fed mice by indirect calorimetry. Interestingly, rDj 1 administration elevated oxygen consumption (VO2) and energy expenditure (EE), while reducing respiratory exchange ratio (RER) without changing food intake or activity (Figures 4N-4Q, 4AA-4GG). Enhanced mitochondrial complex I and complex II activity in isolated liver mitochondria from rDj 1 -treated mice suggest that rDj 1 enhances energy expenditure by increasing mitochondria activity (Figures 4R-4S).

Taken together, these results suggest that rDj 1 enhances mitochondrial respiration and improves energy metabolism in mice to combat HFD feeding-induced hepatic steatosis. Example 6: Djl functional domain is vital to inhibit hepatic steatosis

Dj 1 is a highly conserved protein that is ubiquitously expressed in most mammalian tissues. It belongs to the Dj 1/ThiJ/PfpI family chaperones, and its expression is induced by oxidative stress (20,21). To determine whether the Pfpl domain of Dj 1 exerts a similar role as the full-length Dj 1 protein (rDj 1) in liver cells, truncated Dj 1 (tDj 1) comprising of only the Pfpl domain was purified (Figure 50). HFD-fed mice were intravenous injected with rDj 1 or tDj 1 every other day for 14 days. Intriguingly, both rDj 1 and tDj 1 administration significantly reduced the level of TG in the liver (Figures 5A-5F). In addition, tDj 1 also reduced TG levels, but not NEFA levels, in palmitate acid-treated AML12 cells (Figures 5M and 5N). Consistently, liver histology showed less lipid accumulation in the liver of both rDj l and tDj 1 administrated mice (Figures 5G-5 J, 5P-Q). Both rDj 1 and tDj 1 treatment also improved liver healthy by reducing plasma AST and ALT levels (Figures 5K, 5L). In conclusion, the Pfpl domain of Dj 1 exerts the main role of Dj 1 in inhibiting diet-induced hepatic steatosis.

Example 7: tDjl administration regulates the ASKl-JNK-PPPARa signaling in the liver

As described above, Dj 1 administration stimulates AMPK phosphorylation in the liver cells. However, elevated AMPK phosphorylation in vivo was not observed (data not shown). Numerous studies have reported that the c-Jun N terminal kinase (JNK) is critical to the development of steatosis and chronic liver injury in NAFLD (22-25). Here, JNK (p46 subunit) phosphorylation was significantly reduced in the liver of mice treated with rDj 1 or tDj l, while p38 phosphorylation was only decreased in the liver of tDj 1 -treated mice (Figures 6A-6B), suggesting that Dj 1 targets the mitogen-activated protein kinases (MAPK) pathway in the liver cells. However, not all MAPK pathways were activated. For example, phosphorylation of p42 was not altered by tDj 1 treatment (Figure 60). Both rDj 1 and tDj 1 suppressed TNFa and Anisomycin-induced JNK (p54 and p46) phosphorylation in human HepG2 and mouse AML12 liver cells, respectively (Figures 6C-6D).

A wide variety of mechanisms activate the JNK pathway. In vitro and in vivo studies showed that tDj 1 reduced the phosphorylation of apoptosis signal-regulating kinase 1 (ASK1), but not the transforming growth factor P-activated kinase 1 (TAK1) (Figure 6E, 6P). Moreover, ASK1 is activated by various stresses, including oxidative stress, ER stress, calcium overload, and receptor-mediated inflammatory signals such as TNFa and lipopolysaccharide (LPS) (26,27). rDj 1 administration suppressed both baseline and TNFa- induced ROS levels in HepG2 cells, which may contribute to reducing liver inflammation (Figure 6F). It was found that Dj 1 effectively reduced liver inflammation gene expression and the protein level of cleaved caspase 3 (Figure 6G, 6Q, 6R).

Gene analysis showed that rDj 1 treatment reduced gene expression of de-novo lipogenesis and gluconeogenesis in the liver of NC-fed mice, which were blunted in HFD-fed mice (Figures 6H, 61). Dj 1 treatment increased both mRNA expression and protein levels of peroxisome proliferator-activated receptor alpha (PPARa) in the liver (Figures 6J-JK). Also, the transcriptional activity of PPARa was determined to be elevated by Dj 1 administration in the liver of both NC- and HFD-fed mice (Figures 6L, 6M, 6S, 6T). Furthermore, Dj 1 elevated plasma P-hydroxybutyrate (a ketone body) levels in NC-fed mice but not in HFD-fed mice (Figure 6N, 6U). These findings suggest that Dj 1 inhibits inflammation and liver cell death through the ASKl-JNK-PPARa axis in the liver.

Example 8: tDjl administration ameliorates inflammation and hepatic fibrosis

Selonsertib (ASK1 inhibitor) has failed to reach the primary efficacy endpoint of fibrosis improvement. However, inhibition of ASK1 and its downstream effector JNK1 are promising strategies to reduce liver cell death and hepatic fibrosis in preclinical studies (28- 31). Given Dj 1 inhibits Askl phosphorylation in vitro and in vivo, the impact of tDj 1 on hepatic fibrosis was tested on mice fed a non-alcoholic steatohepatitis (NASH) diet fed for 28 weeks. tDj 1 administration significantly reduced the body weight and improved both glucose and insulin tolerance (Figures 7A-7C). Unlike in HFD-fed mice, tDj 1 did not considerably reduce the TG levels in the liver of the NASH diet-fed mice but significantly suppressed the total cholesterol level in the liver (Figures 7D, 7H, and 7N-7R). More interestingly, tDj 1 administration significantly reduced fibrosis scores (Figures 7E, 7J, 7K) and robustly reduced liver ALT activity but not AST activity (Figures 71, 7S). Consistent with previous findings in the HFD-feeding model, tDj 1 significantly reduced both inflammatory gene expression and liver fibrosis gene expression (Figures 7F, 7L). More strikingly, tDj 1 suppressed hepatic apoptosis, as shown by the TUNEL assay and decreased protein levels of apoptosis markers, including cleaved caspase 3, cleaved caspase 8, cleaved caspase 9, and cleaved PARP protein (Figures 7G, 7M). Together, these findings indicate that tDj 1 administration ameliorates glucose homeostasis and dramatically suppresses inflammation, cellular apoptosis, and fibrosis gene expression in the liver of NASH mice. As an endocrine organ, skeletal muscle produces and secretes hundreds of myokines that allow for crosstalk between the muscle and many other organs (16). The in vitro and in vivo studies presented herein have identified Dj 1 as a novel myokine. Like the concepts of oxidative distress and oxidative eustress, overloaded ER stress is detrimental, while a low dose of ER stress is thought to be necessary for adaptive improvement by exercise and for increasing the health span (13,32,33). Although acute treadmill exercise and chronic running wheel exercise did not elevate plasma Dj 1 levels, it was determined that ER stress, especially Atf6a-Chop activation, could stimulate muscle cells to release Dj 1. Furthermore, consistently elevated circulating Dj 1 in three muscle injury mouse models indicates that muscle cells release of Dj 1 might be a compensatory response to ER stress initiated by muscle injury.

Almost all cells are capable of secreting extracellular vesicles comprising MVBs and exosomes enriched with proteins, nucleic acids, and lipids (14,34). Time-lapse imaging indicated that muscle cells release Dj 1 via shedding vesicles. However, due to the boundaries of imaging and centrifuge procedures, the possibility of Dj l proteins existing in exosomes cannot be excluded.

Dj 1 activated the phosphorylation of AMPK and ACC in HepG2 cells and mouse primary hepatocytes indicating that circulating Dj 1 may regulate energy metabolism in hepatocytes. Although the receptors of Dj 1 on the plasma membrane have not been identified, Dj 1 treatment elevated mitochondrial activity and reduced TG content in liver cells. In vivo studies presented herein consistently showed that Dj 1 administration reduced TG contents in the liver, ameliorated HFD-feeding induced hepatic steatosis, and improved glucose homeostasis and insulin sensitivity. Mitochondria regulate hepatic lipid metabolism and oxidative stress. Accumulating evidence indicates that hepatic mitochondria play a critical role in the development and pathogenesis of steatosis and NAFLD (35,36). Dj 1 administration enhanced the activities of both mitochondrial complex I and complex II, which may be a key contributor to the elevated fatty acid oxidation rate and enhanced energy homeostasis in the liver of mice.

The function of the Pfpl domain of Dj 1, the evolutionarily conserved amino acid sequence of the Dj 1 protein, is not clear (37). Both the full-length recombinant Dj 1 protein (rDj 1) and tDj 1 (only containing the Pfpl domain) exerted similar effects in ameliorating hepatosteatosis, indicating that the Pfpl domain is a critical protein domain of Dj 1 in regulating liver metabolism. ASK1 has been reported to promote inflammation, apoptosis, and fibrosis in the pathogenesis of NASH (29,38). Although selonsertib (ASK1 inhibitor) fails to reach the primary efficacy endpoint of fibrosis improvement (39) in Phase III clinical trial, patients receiving selonsertib demonstrated improvements in the stage of fibrosis, progression to cirrhosis, liver stiffness, and liver fat content in a Phase II trial (28). JNK kinase is one of the key downstream targets of the ASK1 (32), and recent investigations have indicated that the overactivation of JNK is critical to the development of NAFLD, suggesting that JNK may be a novel therapeutic target in NAFLD management (22,25). In vitro and in vivo studies presented herein showed that Dj 1 treatment suppressed the phosphorylation of both ASK1 and JNK but not TAK1, suggesting that Dj 1 specifically inhibited the ASK 1 -JNK pathway in the liver. JNK represses the activity of PPARa, which regulates lipid metabolism in the liver. Gene analysis showed that Dj 1 treatment reduced both de novo lipogenesis (DNL) and gluconeogenesis and elevated plasma P-hydroxybutyrate in the liver of NC-fed mice indicating that Dj 1 administration could enhance lipid oxidation in the liver. However, these changes in gene expressions were not observed in the liver of HFD-fed mice, suggesting that HFD feeding blunts these effects. Moreover, elevated PPARa transcriptional activity was observed in the liver of NC-fed mice treated with rDj 1. These findings indicate that Dj 1 may boost energy metabolism and suppress hepatic steatosis through the ASK 1- JNK -PPARa axis in the liver.

PPARa activation, in combination with PPARp/6 agonism, can reduce inflammation and reverse mild liver fibrosis. Indeed, Dj 1 administration improved glucose homeostasis and insulin action, reduced inflammation, inhibited cell apoptosis, and suppressed fibrosis gene expression in the liver of the mouse NASH model. The findings suggest that Dj 1 may ameliorate hepatic inflammation, apoptosis, and fibrosis through the ASKl-JNK-PPARa pathway. Altogether, these findings indicate that Dj 1 is a potential therapeutic agent for treating NAFLD.

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Claims

We claim:

1. A method of treating a metabolic disorder comprising administering to a patient in need thereof a therapeutically effective amount of a Dj 1 polypeptide or fragment thereof or a nucleic acid molecule encoding a Dj 1 polypeptide or fragment thereof.

2. The method of claim 1, wherein the metabolic disorder is selected from non-alcoholic fatty liver disease (NAFLD), steatohepatitis, type II diabetes, hyperglycemia, hyperlipidemia, dyslipidemia, obesity, hyperinsulinemia, insulin resistance, hypercholesterolemia, non- familial hypercholesterolemia, familial hypercholesterolemia, heterozygous familial hypercholesterolemia, homozygous familial hypercholesterolemia, mixed dyslipidemia, atherosclerosis, early onset coronary heart disease, dyslipidemia, hypertriglyceridemia, hyperfattyacidemia, and cirrhosis.

3. A method of reducing fat accumulation in the liver comprising administering to a patient in need thereof a therapeutically effective amount of a Dj 1 polypeptide or fragment thereof or a nucleic acid molecule encoding a Dj 1 protein or fragment thereof.

4. The method of claim 3, wherein the Dj 1 polypeptide or fragment thereof or the nucleic acid molecule encoding a Dj 1 protein or fragment thereof is co-administered with a therapeutically effective amount of a lipid-lowering agent.

5. The method of claim 4, wherein the lipid-lowering agent is selected from atorvastatin, simvastatin, rosuvastatin, fluvastatin, ezetimibe, niacin, bezafibrate, ciprofibrate, clofibrate, gemfibrozil, and fenofibrate.

6. A method of reducing blood glucose levels comprising administering to a patient in need thereof a therapeutically effective amount of a Dj 1 polypeptide or fragment thereof or a nucleic acid molecule encoding the Dj 1 protein or fragment thereof.

7. The method of claim 6, wherein the Dj 1 polypeptide or fragment thereof or the nucleic acid molecule encoding the Dj 1 protein or fragment thereof is co-administered with a therapeutically effective amount of insulin, GLP-1, metformin, or a DPP4 inhibitor.

8. The method of any one of claims 1-7, wherein the Dj 1 polypeptide comprises an amino acid sequence having at least 70% sequence identity to SEQ ID NO: 1, 3, or 4.

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9. The method of any one of claims 1-8, wherein the Dj 1 polypeptide comprises amino acid residues 32-173 of SEQ ID NO: 1.

10. The method of any one of claims 1-8, wherein the Dj 1 polypeptide consists of an amino acid sequence having at least 70% sequence identity to SEQ ID NO: 3.

11. The method of any one of claims 1-8, wherein the amino acid sequence of the Dj 1 polypeptide is at least 85% identical to SEQ ID NO: 1, 3, or 4.

12. The method of any one of claims 1-7, wherein the nucleic acid molecule encoding the Dj 1 polypeptide comprises a nucleic acid sequence having 70% identity to the nucleic acid sequence of SEQ ID NO: 2 or 5.

13. The method of any one of claims 1-12, wherein the Dj 1 polypeptide or fragment thereof or the nucleic acid molecule encoding the Dj 1 protein or fragment thereof is chemically synthesized or purified from recombinant sources.

14. A composition comprising: a Dj 1 polypeptide or fragment thereof or a nucleic acid molecule encoding the Dj 1 protein or fragment thereof; and a pharmaceutically acceptable carrier, wherein the Dj 1 polypeptide or fragment thereof comprises an amino acid sequence at least 70% identical to SEQ ID NO: 1, 3, or 4; or wherein the nucleic acid molecule encoding the Dj 1 polypeptide or fragment thereof comprises a nucleic acid sequence that is at least 70% identical to SEQ ID NO: 2 or 5.

15. The composition of claim 14, wherein the Dj 1 polypeptide has the amino acid sequence of SEQ ID NO: 3.

16. A method of detecting muscle injury in a subject, the method comprising determining a Dj 1 polynucleotide or polypeptide level in a sample from the subject, wherein an elevated Dj 1 polynucleotide or polypeptide level in the subject relative to a reference or control is indicative of muscle injury.

17. A method for determining susceptibility to muscle injury in a subject, the method comprising determining a Dj 1 polynucleotide or polypeptide level in a sample from the subject, wherein an increased Dj 1 polynucleotide or polypeptide level in the subject relative to a reference or control indicates that the subject is susceptible to muscle injury.

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18. The method of claim 16 or 17, wherein the reference is a previously determined level of the Dj 1 polynucleotide or polypeptide from a normal subject.

19. The method of claim 16, or 17 wherein the control is the Dj 1 polynucleotide or polypeptide level in a normal subject that has not suffered muscle injury.

20. A method for determining susceptibility to a muscle injury in a subject, the method comprising determining at least a first Dj 1 polynucleotide or polypeptide level in a first subject sample and a second Dj 1 polynucleotide or polypeptide level in a second subject sample, wherein an elevated second Dj 1 polynucleotide or polypeptide level relative to the first Dj 1 polynucleotide or polypeptide level is suggestive of susceptibility to the muscle injury.

21. A method for determining the progression of muscle injury in a subject, the method comprising determining more than one Dj 1 polynucleotide or polypeptide level in subject samples over time, wherein an increase in the Dj 1 polynucleotide or polypeptide levels over time is indicative of muscle injury progression.

22. The method of any one of claims 16-21, wherein the muscle injury is a symptom of a disease or condition selected from amyotrophic lateral sclerosis, Charcot-Marie-Tooth disease, multiple sclerosis, muscular dystrophy, myasthenia gravis, myopathy, myositis, peripheral neuropathy, spinal muscular atrophy, cardiac myopathy, rhabdomyolysis, myasthenia gravis, fibrositis, cramp, and sarcopenia.

23. The method of any one of claims 16-22, wherein the Dj 1 polypeptide level is a measure of serum protein concentration of the Dj 1 polypeptide.

24. The method of any one of claims 16-22, wherein the Dj 1 polynucleotide level is a measure of PARK7 mRNA levels.

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