Methods for diagnosing or monitoring muscular dystrophies

Abstract

The invention relates to a method for prognosing, diagnosing, determining the risk, and monitoring the evolution of a muscular dystrophy. It also relates to a method for evaluating the efficacy of a treatment of a muscular dystrophy in a subject in need thereof.

Claims

1. A method for detecting myomesin 2 protein or myomesin 3 protein in a biological fluid from a subject comprising detecting the presence or absence of myomesin 2 protein or myomesin 3 protein in a sample of biological fluid of said subject, said detecting comprising: a) contacting said sample of biological fluid with antibodies that bind to an epitope of myomesin 2 or myomesin 3 and detecting the binding of said antibodies to said epitope; or b) specifically quantifying myomesin 2 protein or myomesin 3 protein in said sample of biological fluid by mass spectroscopy, wherein the biological fluid is blood, serum, plasma, saliva or urine.

2. The method according to claim 1, said method comprising: measuring the level of the myomesin 2 protein or myomesin 3 protein in a biological fluid sample of the subject, and comparing this level to the level of said myomesin 2 protein or myomesin 3 protein in a biological fluid sample previously collected from the same subject.

3. The method according to claim 2, comprising: a) determining a reference level of the myomesin 2 protein or myomesin 3 protein by measuring the level of said myomesin 2 protein or myomesin 3 protein in a biological fluid sample of the subject; and b) determining a test level of myomesin 2 protein or myomesin 3 protein by measuring the level of said myomesin 2 protein or myomesin 3 protein in a second biological fluid sample collected from the same subject at a time after administration of a treatment.

4. The method according to claim 2, said method comprising treating a subject having muscular dystrophy and measuring the level of the myomesin 2 protein or myomesin 3 protein in a biological fluid sample of the subject after the treatment and comparing the level of the myomesin 2 protein or myomesin 3 protein after the treatment to the level of said myomesin 2 protein or said myomesin 3 protein in a biological fluid sample previously collected from the same subject prior to treatment.

5. The method according to claim 1, wherein the biological fluid is serum.

6. The method according to claim 1, said method comprising detecting the presence or absence of one or more polypeptide fragments of myomesin 3 in a sample of biological fluid of said subject, said one or more polypeptide fragments being a fragment of amino acids 350 to 1350 of SEQ ID NO: 1, said detecting comprising: a) contacting said sample of biological fluid with antibodies that bind to an epitope of said one or more fragments and detecting the binding of said antibodies to said epitope; or b) specifically quantifying said one or more fragments in said sample of biological fluid by mass spectroscopy.

7. The method according to claim 6, wherein the one or more fragments of myomesin 3 protein is selected from SEQ ID NO:2 to SEQ ID NO:16.

8. The method according to claim 1, comprising detecting the presence or absence of one or more C-terminal fragments of myomesin 3 protein, in a sample of biological fluid of said subject, said detecting comprising: a) contacting said sample of biological fluid with antibodies that bind to an epitope of said one or more C-terminal fragments and detecting the binding of said antibodies to said epitope; or b) specifically quantifying said one or more C-terminal fragments in said sample of biological fluid by mass spectroscopy, wherein the biological fluid is blood, serum, plasma, saliva or urine.

9. The method according to claim 8, wherein the one or more C-terminal fragments of myomesin 3 protein is a fragment of about 110 or 140 kDa.

10. The method according to claim 1, wherein the biological fluid is obtained from a subject having a family history of a muscular dystrophy.

11. The method according to claim 1, wherein the biological fluid is obtained from a subject having a muscular dystrophy.

12. The method according to claim 1, wherein the biological fluid is obtained from a subject having undergone genome analysis and having been identified as having a predisposition to a muscular dystrophy on the basis of the genome analysis.

Description

LEGENDS OF THE FIGURES

(1) FIG. 1: Analysis of Myomesin 3 in sera from healthy subjects and DMD patients by Western blot. Antibodies against C-ter part of myomesin-3 revealed the presence of both 140 kDa and 110 kDa fragments exclusively in serum samples from DMD patients which correlates with the mass spectrometry LC/MS/MS analysis.

(2) FIG. 2: Analysis of Myomesin 3 in sera from dogs and mice by Western blot. Western blot analysis of sera from animal models of DMD (GRMD dog and mdx mouse) revealed the presence of the myomesin-3 exclusively in sera from the affected animals.

(3) FIG. 3: Analysis of Myomesin 3 and CK in sera from 1 day-old healthy and mdx mice by Western blot. Serum from 5 healthy and 5 mdx mice was used in this experiment. Myomesin-3 fragments are detectable at the low level in all of the five mdx tested. Importantly, there is no correlation between CK level and Myomesin 3 level in the studied animals: CK was detected in all samples while myomesin 3 only in mdx mice. Moreover, some healthy mice demonstrated higher CK level compared to those in “low level CK” mdx mice (see healthy mice 3 and 5 and mdx mice 2 and 5).

(4) FIG. 4: Analysis of Myomesin 3 and CK in sera from mdx and healthy mice at different ages by Western blot. Analysis of MYOM3 and creatine kinase was performed by Western blot on sera from 10 healthy controls and 10 mdx mice. Samples were taken each week starting from 1-week of age. Gray crosses indicate that there was no serum available for these mice.

(5) FIG. 5: Constant level of Myomesin 3 and variable level of CK in sera from mdx and healthy mice after physical exercise. Analysis of MYOM3 and creatine kinase was performed by Western blot on sera from two groups of mice (healthy controls and mdx). Six 3 month-old mice were subjected to an intense physical exercise on a homemade treadmill. Serum samples were collected 7 days before exercise and 3 h, 24 h, 48 h after exercise.

(6) FIG. 6: MYOM3 fragments in sera of LGMD2D patients. Upper panel: Western blot analysis of MYOM3 in sera from LGMD2 patients (1-3) and controls (4-5). Lower panel: CK assays on the same sera. The activity was measured in international system unit per liter (U/L).

(7) FIG. 7: Constant level of MYOM3 fragments in serum of KO-Sgca mice after physical exercise. Western blot analysis of MYOM3 in sera from a group of KO-Sgca mice at different time of the Escape test (“Escape”) (D0: 6 days before the exercise, D6: 20 min after the exercise, and D7: 24 hours after exercise). “Rest”: the same time points for the control group of mice not subjected to physical exercise (n=3). The level of the MYOM3 stays stable at any time point.

(8) FIG. 8: Gene therapy of KO-Sgca mice decreases the level of MYOM3 fragments in serum. Mice were systemically injected either with PBS or with 1e11vg or 5e11vg of rAAV coding for wt human alpha-sarcoglycan (n=6 for each group), At days 14.sup.th and 56.sup.th after injections serum was taken for the analysis of CK and MYOM3. Before the endpoint of the experiment (56 days after injection, at age of 90 days) muscle force was estimated by the escape test. At the end point mice were sacrificed and gastrocnemius anterior muscle transverse sections were characterized by HPS staining and the presence of SGCA were analysed with antibody against SGCA. A: Upper panel: Western blot analysis of MYOM3 and CK 14 days after rAAV treatment. Two representative analyses are presented for each group. Lover panel: Graph representation of the MYOM3 and CK level in each group 14 days after rAAV treatment. Each spot on the graph correspond to one animal. B: Upper panel: Western blot analysis of MYOM3 and CK 56 day after rAAV treatment. Two representative analyses are presented for each group. Lower panel: Graph representation of the MYOM3 and CK level in each group 56 days after rAAV treatment. Each spot on the graph correspond to one animal. C: Histochemical characterization of gastrocnemius anterior muscles from treated and control mice 90 days after rAAV injection. D: Correlation between the serum level of MYOM3 fragments and muscle force after gene therapy treatment. Plots show relationships between MYOM3 and muscle force and between CK and muscle force. The level of MYOM3 fragments are in a good correlation with the restoration of the muscle morphology and physical force.

(9) FIG. 9: MYOM3 fragments in serum of other muscular diseases. Analysis of MYOM3 was performed by Western blot in sera from mice models for different dystrophies (KO-Sgca, MDX, KO-Dysf, KO-Capn3 and KO-Sgcg) and controls (C57B16) at the age of 4 weeks and 6 months. The high level of MYOM3 fragments were found at the both ages in MDX, KO-Sgca and KO-Sgcg mice while in KO-Dysf these fragments were barely detectable at 1 month age and reached its maximum at the age of 6 month. Only a faint labelling of MYOM3 fragment was detected in KO-Capn3 mice.

(10) FIG. 10: List of Myomesin-3 peptides identified by mass spectrometry in sera from 4 DMD patients (SEQ ID NOs: 2-16, respectively). Only peptides with an ion score higher than 30 at least in one DMD patient are shown.

(11) FIG. 11. Western blot analysis of MYOM3 in sera from subgroups of young (G1) and older (G3) DMD patients as well as young (G3) and older (G4) healthy subjects. A: normal exposure; B: boosted exposure. For explanation of groups and subgroups see Table 1. Fifty micrograms of serum proteins was loaded in each well.

(12) FIG. 12. Expression levels of serum MYOM3 fragments (A) and CK (B) in sera from the entire US cohort including 39 young and 17 older DMD patients as well as 29 young and 18 older healthy controls. To measure levels of the MYOM3 fragments, 50 μg of serum proteins were analysed by Western blot, then band intensities were quantified and expressed in arbitrary units (a.u). The CK enzyme activity in serum is expressed in international units per litre (IU/L). (C) Linear regression analysis between serum levels of the MYOM3 fragments and CK for young patients. (D) Linear regression analysis between serum levels of the MYOM3 fragments and CK for older DMD patients.

(13) FIG. 13. MYOM3 fragments are specifically present in sera from animal models of DMD. A: Western Blot analysis of serum from GRMD and healthy dogs. GRMD #1-4: two month old; #5-6: 18 months old. Healthy #1-4: two months old; #5-6: 18 months old dogs. DMD: control serum from DMD patient. B: Western Blot analysis of serum from 6 months old mdx and WT mice. WT: C57/BL10 strain.

(14) FIG. 14. A: Western blot analysis of the MYOM3 fragments in serum from 3 LGMD2D patients (#1 is 35, #2 is 23 and #3 is 24 years old). Serum from 2 DMD patients (group G1) and 3 healthy individuals (group G4) were used as controls. B: Western blot analysis of the MYOM3 fragments in serum from mouse models of different muscular dystrophies at 1 and 6 months of age. WT: C57BL/6J mouse; mdx (model for DMD); KO-Sgcg: model for LGMD2C; KO-Sgca: model for LGMD2D; KO-Dysf: model for LGMD2B; KO-Capn3: model for LGMD2A.

(15) FIG. 15. Levels of the MYOM3 fragments (A, B) and CK-M (C, D) in serum from healthy (B, D) and mdx (A, C) mice at different ages as estimated by Western blot analysis. Intensity of the bands (in arbitrary units, a.u.) on different gels was normalised by the respective bands of the positive control (50 μg of serum proteins from the same mdx mouse present on each gel). Fifty micrograms of serum proteins was used for the analysis. Age 0 corresponds to newborn mice. Estimation of the CK-M level by Western blot analysis correlated well with the CK activity (FIG. 20).

(16) FIG. 16. Levels of the MYOM3 fragments (A, B) and CK-M (C, D) in serum from healthy (B, D) and mdx (A, C) mice at different time after physical exercise estimated by Western blot analysis. Band intensity on different gels was normalised by the respective bands of the positive control (50 μg of serum proteins from the same mdx mouse present on each gel). Fifty micrograms of mouse serum was used for the analysis.

(17) FIG. 17. Effect of antisense oligonucleotide-mediated exon skipping therapy in mdx mice on the serum levels of the MYOM3 fragments and CK-M. Four 12 weeks aged mdx mice received a single 12.5 mg/kg tail vein injection of Pip6a-PMO. Blood samples from the injected mdx mice were collected at 14, 16 and 20 weeks of age (2, 4 and 8 weeks post-injection) and from the control mice at 14 and 20 weeks of age. Levels of the MYOM3 fragments and CK-M were estimated by Western blot analysis.

(18) FIG. 18. Comparison of different assays for the follow up of the gene therapy treatment in KO-Sgca mice. A: Histological analyses (upper panel: Hematoxylin Phloxine Saffron stain; lower panel: immunodetection of α-sarcoglycan) of gastrocnemius muscles after treatment with increasing doses of rAAV coding for huSgca (1e11, 5e11, and 1e12 vg). B: Quantitative analysis of α-sarcoglycan positive fibres after the treatments. C: Restoration of muscular strength (escape test) 83 days after the treatment. D: Serum CK and E: MYOM3 fragments levels at different time after the treatment (mean±SEM). F: Raw P-values (Student's t test) for the comparison of MYOM3 and CK levels between different groups of mice at different time points. The values below the threshold 0.01 are in pink, and below 0.05 are in yellow. KO_PBS, KO_1e11, KO_5e11, KO_1e12: KO-Sgca mice injected with PBS or the respective dose of the vector. WT_PBS: C57BL/6J control mice injected with PBS. Levels of the MYOM3 fragments and CK-M were estimated biweekly by Western blot analysis.

(19) FIG. 19: Correlation between the levels of the MYOM3 fragments (A) or CK-M (B) in serum with muscle force evaluated by the escape test. KO_PBS, KO_1e11, KO_5e11, KO_1e12: KO-Sgca mice injected with PBS or the respective dose of the vector. WT_PBS: C57BL/6J control mice injected with PBS. Levels of the MYOM3 fragments and CK-M were estimated by Western blot analysis 78 days post-injection. Dpi: days post-injection.

(20) FIG. 20: Correlation between the CK-M measured by Western blot (a.u) and its enzymatic activity (IU/L). Level of CK was measured by two methods in serum of mdx mice before and at different time after physical exercises. Three mice and four time points were used to build the graph.

(21) FIG. 21: Effect of physical exercise on the level of the MYOM2 fragments in serum from mdx mice. Serum samples were taken 7 days before and 3, 24 and 48 hours after the exercise. Upper panel: Western blot analysis with anti-Myom2 antibodies; lower panel: quantification of the myom2 expression. MYOM2: position of the myom2 fragments. One microliter of serum was used for the analysis.

EXAMPLES

Example 1

(22) Material and Methods

(23) Serum Depletion

(24) Using the manufacturer instructions, 10 microliters of serum (6 healthy donors and 4 DMD patients) were depleted with an affinity depletion column that selectively removes 12 of the most abundant proteins (“Proteome purify 12” kit from R&D System). Then, 300 μl of depleted solution was precipitated with 4 volumes of acetone 100% overnight at 4° C. followed by centrifugation at 14000 g for 10 minutes at 4° C. The pellet was resuspended in 50 μl buffer containing 6M urea/2M thiourea and protein concentration was determined by Bradford assay.

(25) Mass Spectrometry (LC-MS/MS) Analysis

(26) A volume of serum containing ten micrograms of proteins was adjusted to 120 μl of the reaction mixture containing 4 M urea, 1.5 M thiourea and 50 mM tris-HCl pH 8.3. Proteins were reduced with 10 mM dithiothreitol for 30 min and then alkylated with 55 mM iodoacetamide for 20 min. Alkylated proteins were digested firstly with 500 ng of endopeptidase lys-C (Wako) for 3 h at room temperature (RT). Then, the mixture was diluted with 3 volumes of MilliQ-water and treated with 500 ng of trypsin (Sequence Grade Trypsin, Promega) for 16 h at RT. Enzymatic activity was stopped by addition of formic acid to a final concentration of 3%. Samples were stored at −20° C. until use.

(27) Peptide mixture was desalted using ZipTip.sub.μ-C18 Pipette Tip (Millipore) and separated with an Easy nano-LC Proxeon system (Thermo Fisher Scientific) equipped with a reversed phase C18 column (Easy-Column Proxeon C18, L 10 cm, ID 75 μm, 120 Å) with the following parameters: 300 nl/min flow, gradient rising from 95% solvent A (0.1% formic acid) to 25% B (100% acetonitrile, 0.1% formic acid) in 20 min, then to 45% B in 40 min and finally to 80% B in 10 min. Eluates were monitored by a LTQ Velos Orbitrap mass spectrometer (Thermo Fisher Scientific) in full ion scan mode at a resolution of 30,000 and a mass range of 400-1,800 m/z. The mass spectrometer was operated in a data dependent manner, selecting the 20 most intense precursor ions with a dynamic exclusion of 15 sec (isolation width of 1 Da and activation of 0.250 for 10 ms) for sequential fragmentation by collision induced dissociation (collisional energy of 40%).

(28) Data were processed with Proteome Discoverer 1.4 software (Thermo Fisher scientific) coupled to an in house Mascot search server (Matrix Science, 2.3.2 version) using SwissProt database and the following parameters: human/mouse/dog species, mass tolerance of 10 ppm for precursor ions or 0.6 Da for fragments, and two missed cleavage site. Partial chemical modification such as oxidation of methionine and carbamidomethylation of cysteine were taken into consideration for the queries. False discovery rate was estimated using a reversed database search approach.

(29) Vector Construction and Production

(30) A plasmid carrying the coding sequence of human α-sarcoglycan was obtained from Dr. Jeng-Shin Lee (HGTI, Harvard). It was used to construct the pAAV.Des. SGCA 142T plasmids that consist of an AAV-based pSMD2-derived vector (Snyder, 1997) where the human α-sarcoglycan is placed under the control of a human Desmin promoter and 4 repeats of the miR-142-3p target sequences described in (Brown et al., 2006). Plasmids were prepared using the Nucleobond PC2000EF kit from Macherey-Nagel (Germany). The integrity of the constructs was confirmed by sequencing. Adenovirus free AAV2/8 viral preparations were generated by packaging AAV2-ITR recombinant genomes in AAV8 capsids using a three plasmid transfection protocol (Bartoli, 2006). After DNA extraction by successive treatments with DNAse I and proteinase K, viral genomes were quantified by a TaqMan real-time PCR assay using primers and probes corresponding to the ITR region and to the albumin gene (Alb) for normalization of the data across samples. The primer pairs and TaqMan MGB probes used for ITR amplification were: 1AAV65/Fwd: .sub.5′CTCCATCACTAGGGGTTCCTTGTA.sub.3′ (SEQ ID NO:17), 64AAV65/rev: .sub.5′TGGCTACGTAGATAAGTAGCATGGC.sub.3′ (SEQ ID NO:18) and AAV65MGB/taq: .sub.5′GTTAATGATTAACCC.sub.3′ (SEQ ID NO:19). The primer pairs and TaqMan MGB probes used for Alb amplification were: ALB.Fwd: .sub.5′GCTGTCATCTCTTGTGGGCTGT.sub.3′ (SEQ ID NO:20), ALB.Rev: .sub.5′ACTCATGGGAGCTGCTGGTTC.sub.3′ (SEQ ID NO:21) and AlbVic/taq: 5′CCTGTCATGCCCACACAAATCTCTCC.sub.3′ (SEQ ID NO:22).

(31) Animal Models, Blood Sampling and Vector Administration

(32) The mouse strains included in this study are shown in Table 1. All animal procedures were performed in accordance with the directive of 24 Nov. 1986 (86/609/EEC) of the Council of the European Communities and were approved by Genethon's ethics committee under the number CE12-034. C57BL/6 mice were purchased from Charles River Laboratories (Les Oncins, France). Sgca_null (KO-Sgca) mice were obtained and bred at Généthon's animal facility. Mice were handled according to A1 biosafety requirements in accordance with the European guidelines for use of experimental animals. All experiments were performed accordingly to minimize animal discomfort. Prior to blood extraction, mice were anesthetized by intraperitoneal injection of ketamine/xylazine. Anesthetized mice were sacrifice by cervical elongation at the end of the experiments.

(33) All experimental gene transfer protocols were performed on 4 week-old male mice. Systemic administrations were performed by tail vein injections of 500 μl of solution containing different quantities of rAAV (1e11 or 5e11 viral genome(vg)/mouse) or Phosphate-Buffered Saline (PBS; Gibco, Life Technologies). Samples were taken for the analysis at 14.sup.th and 56.sup.th days after injection. Blood was collected by retro-orbital puncture of anesthetized animals.

(34) TABLE-US-00001 TABLE 1 Principal features of mouse strains of muscular dystrophy models Name Official name Mutation reference Localisation KO-Capn3 B6- KO-CAPN3 Laure, et al.; FEBS GNT Capn3.sup.tm2.1Gnt partial out-of-frame J. 2009 deletion KO-Dysf B6.A- insertion Lostal, et al.; Hum GNT Dysf.sup.prmd/J transposon Mol Genet. 2010 KI-FKRP B6; 129- KI-FKRP Cerfe FKRP.sup.tm1Gnt L276I KO-Sgca B6-Sgca.sup.tm1Kcam KO-SGCA Duclos, et al; J Cell GNT partial out-of- Biol. 1998 frame deletion KO-Sgcg B6-Sgca.sup.tm1Kcam KO-SGCG Hack AA, et al; J GNT partial out-of- Cell Biol. 1998 frame deletion MDX B6Ros.Cg- C-to-T Chapman VM, et al; Charles River Dmd.sup.mdx-4Cv/J transition at PNAS. 1989 Laboratories position 7916 (DYS exon 53) WT C57Bl/6 Charles River Laboratories

(35) Physical Exercise

(36) Two groups (healthy controls and mdx) of six 3 month-old mice were placed on a homemade treadmill to run with a downstairs inclination of 15° at the speed of 8 m/min for 5 min, followed by 12 m/min for 25 min. Serum samples were collected 7 days before exercise and 3 h, 24 h, 48 h after exercise and stored at −80° C.

(37) Aging

(38) Serum samples of 10 healthy controls and 10 mdx mice from 1-week up to 4-week-old were collected each week and stored at −80° C. Serum samples from 1 day-old mice (5 healthy controls or 5 mdx) were collected after euthanasia.

(39) Escape Test

(40) Mouse muscle force was evaluated by the “escape test” (Carlson, 1990). Mice were placed on a platform facing the entrance of a tube that was 30 cm long. A cuff was wrapped around the tail and connected to a fixed force transducer. In response to gentle pinching of the tail, mice tried to escape within the tube. This was prevented by attaching the tail to the force transducer and a short peak of force was recorded. Maximal peak and the average of the five highest peaks normalized to animal body weight are reported. Sera were obtained from Blood samples by retro-orbital puncture of anesthetized animals. All mice were received an intraperitoneal injection of Evans blue dye (EBD) (1 mg/g of body weight) 5 hours after the test. The mice were sacrificed 24 hours after EBD injection and the TA muscles were removed and quickly frozen in liquid nitrogen-cooled isopentane.

(41) Serum Creatine Kinase Activity Measurement

(42) The creatine kinase (CK) activity in serum was measured using VITROS CK Slides (Ortho-Clinical Diagnostics, Johnson & Johnson).

(43) Western Blot Analysis

(44) Protein samples were separated by SDS-PAGE electrophoresis (4 to 12% gradient, NuPAGE Novex Bis-Tris Gel 1.0 mm, Life Technologies) and transferred onto an Immobilon-P Transfer Membrane (Millipore). Fifty micrograms of human, dog or mouse of serum protein were loaded per line. A Rabbit polyclonal antibody (pAb) to Myomesin-3 (1:1000; 17692-1-AP: Proteintech) and a goat polyclonal antibody to human CK-M (N-13, 1/500, Santa Cruz) were used as primary antibodies followed by corresponding IRDye-800CW-conjugated antibodies (1:10,000) according to the manufacturer's instructions (Li-Cor Biosciences). Infrared fluorescence of the secondary antibodies was read on an Odyssey Imaging System (LI-COR Biosciences). The Precision Plus Protein Standards (Bio-Rad) were used as molecular weight markers. Band intensities were measured by the Odyssey application software (LI-COR Biosciences, 2.1 version).

(45) Histology and Immunostaining

(46) Cryosections (8 μm thickness) were prepared from frozen muscles. Transverse sections were processed for hematoxylin phloxine saffron (HPS) staining and α-sarcoglycan immunostaining.

(47) For colorimetric immunodetection of α-sarcoglycan, unfixed transverse cryosections were rehydrated with PBS for 5 min and then incubated with H.sub.2O.sub.2 for 20 min at room temperature (RT) to inhibit endogenous peroxidases. After washing with PBS, sections were blocked with PBS/10% goat serum for 30 min and then incubated with 1/1000 dilution of a rabbit polyclonal primary antibody directed against amino acids 366-379 of the human α-sarcoglycan sequence (AC-ahSarco57) 1 to 2 h at RT. After washing with PBS, sections were incubated with secondary antibody conjugated with horseradish peroxidase (HRP) diluted 1/200 for 1 h at RT. Sections were washed 3 times with PBS and then incubated with diluted diaminobenzidine (DAB; DAKO) for 2-5 min. Then, sections were successively treated with ethanol (5 min), twice in xylene (5 min), mounted with Eukkit (Labonord, France) and visualized on a Nikon microscope.

(48) Results

(49) Dystrophin

(50) Identification of Myomesin 3 Fragments in Sera of DMD Patients by Mass-Spectrometry

(51) Mass spectrometry (LC-MS/MS) analysis of 4 DMD patients and 6 healthy controls revealed the presence of myomesin 3 exclusively in the DMD samples. Peptides matching myomesin-3 were detected in 3 from 4 DMD patients (FIG. 10). Apart a gap of the first 300 amino acids, peptides were distributed all along the myomesin-3 protein (FIG. 10).

(52) Myomesin 3 is a 162 kDa structural protein localised on the M line of the sarcomere in striated skeletal muscles. It belongs to the myomesin family further comprising myomesin 1 and myomesin 2 (M protein). These proteins are composed mainly of immunoglobulin-like and fibronectin domains (a unique N-terminal domain, two Ig domains (Ig2-3), 5 Fn domains (Fn4-8) and 5 C-terminal Ig domains (Ig9-13). It has been shown that they bind to myosin by their N-terminus and titin by their central part and that they dimerize by their C-terminus. A binding of the M protein and myomesin with creatine kinase has also been reported. Myomesin 3 is found in skeletal muscle and appears to be specifically expressed in the fibers of the intermediate type and to a lesser extent in the slow fibers. These proteins are involved in sarcomere structure allowing anchoring of myosin and titin to the line M. They also allow sarcomeres to withstand the mechanical stresses thanks to their elastic properties.

(53) Presence of Myomesin 3 Fragments in the Serum of Patients with Duchenne Muscular Dystrophy

(54) Western blot analysis with antibodies against the C-terminal part of myomesin 3 showed the presence of two fragments of 110 kDa and 140 kDa in the sera of patients with Duchenne dystrophy (FIG. 1). These fragments were undetectable in all healthy subjects. Five patients with Duchenne muscular dystrophy have been analyzed so far.

(55) Presence of MYOM3 Fragments in Sera of GRMD Dogs

(56) Western blot analysis of sera from canine model of DMD (GRMD dog) revealed the presence of two bands migrating at the same positions as C-ter fragments of human MYOM3 (FIG. 2). A total of 40 dogs GRMD and 30 healthy controls aged from 40 days to 1 year and a half have been tested. These fragments were exclusively present in sera from all the affected animals.

(57) Presence of MYOM3 Fragments in Sera of Mdx Mice

(58) The presence of the MYOM3 fragments was analyzed on mice aged 1 week to 1 year by Western blot analysis. The fragments were detected in all mdx mice at all ages tested (from 1 day to 6 months: FIGS. 3, 4 and 10) and were absent in the healthy controls (a total of about 100 mdx and 100 control mice were tested). Interestingly, the level of MYOM3 in the sera increased progressively with mouse aging and did not correlate with the timing of the acute phase of muscle necrosis, which occurs generally at three to four weeks of age, followed by an apparent stabilisation of the mouse phenotype. The kinetic of creatine kinase level is quite different from those of MYOM3: firstly, there are substantial inter-individual variations in the CK level; secondly the high level of CK was already seen at the birth (1 day of age), but at one week age CK was undetectable, raising again at 2 week and further augmenting at 4 weeks age (FIGS. 3, 4). Importantly, the level of CK at birth can be higher in the healthy controls compared to mdx mice (FIG. 2).

(59) Similarity in the MYOM3 fragment sizes between different species could imply similar mechanisms of myomesin-3 processing in this dystrophy.

(60) Steady Level of the MYOM3 Fragments in the Serum of mdx Mice Subjected to Physical Exercise.

(61) To follow the impacts of physical exercise on myomesin-3 and creatine kinase levels in sera, healthy and mdx mice were subjected to downhill running for 30 min. All 6 healthy mice were able to run during 30 min without signs of wearing. In contrast, only 1 mdx mouse was able to complete the exercise (mdx n° 1) while the others stopped after 10 min (2 mice) or 15 min (3 mice). The fragments of MYOM3 were present at all time-points in serum from mdx mice with only a slight increase of intensity at 24 h and 48 h, while the level of CK varied substantially being at least four times higher 3 hours post-exercise compared to the level before the exercise (FIG. 5). Importantly MYOM3 fragments were not detected in serum of healthy controls while creatine kinase was detected at different levels in serum of all healthy mice without noticeable correlation with physical exercise. In conclusion, the analysis of the impact of exercise (treadmill running) on the presence of myomesin-3 fragments in the serum of mdx mice showed no increase in these fragments after exercise unlike the increase in creatine kinase.

(62) Alpha-Sarcoglycan

(63) The Fragments of Myomesin 3 are Present in the Sera of LGMD2D Patients.

(64) In order to know whether the presence of MYOM3 in serum is a specific feature of DMD patients or this protein can be also detected in serum from patients with other dystrophic muscle diseases, we analyzed serum from 3 available LGMD2D patients. Western blot analysis demonstrated that MYOM3 fragments of the same size as in DMD patients were present in the sera of all of the three patients (FIG. 6), while no fragments were seen in the healthy controls.

(65) Stable Presence of Fragments in the Serum of KO-Sgca Mice Subjected to Physical Exercise (Alpha-Sarcoglycanopathy Model).

(66) The presence of these fragments was analyzed by Western blot at rest and at different time points after muscular effort (escape test) (FIG. 7). The level of MYOM3 fragments after exercise stayed at the same level as at rest.

(67) The Level of Myomesisn-3 Fragments in Sera Correlates with the Efficiency of Gene Transfer and Mouse Muscle Strength.

(68) We then analyzed the level of myomesin-3 fragments in sera after gene therapy of the KO-Sgca mice. To this goal KO-Sgca mice received intravenous injection with two different doses (1e11 and 5e11 viral genomes (vg)) of AAV8 coding for human alpha-sarcoglycan (SGCA) under the control of desmin promoter. The efficiency of the therapy was evaluated by immunostaining of Sgca and by hematoxylin phloxine saffron (HPS) stain on muscle sections 56 days after rAAV8 injections (FIG. 8). At the low vector dose about 10% of the fibers expressed SGCA, while at the highest dose 90% of the fibers were SGCA-positive. The HPS stain confirmed the improvement of muscle morphology with the increase of the vector doses. Importantly, the level of MYOM3 fragments in sera of KO Sgca mice decreased with the increase in the efficiency of gene transfer. This effect was already visible 14 days after AAV injection and persisted after 56 days post-injection. Correlation analysis between the mouse muscle force measured by Escape Test and the level of serum MYOM3 fragments demonstrated a tight correlation between these values (r2=0.7616). No statistically significant correlation was found between muscle force after gene therapy and serum CK level (r2=0.2619) (FIG. 8).

(69) Other Diseases

(70) Presence of Myomesin 3 Fragments in Serum From Mouse Models of Other Dystrophies.

(71) Analysis of MYOM3 was performed by Western blot in sera from mice models for different dystrophies (KO-Sgca, MDX, KO-Dysf, KO-Capn3 and KO-Sgcg) and controls (C57B16) (see Table 1 for the description of models) at the age of 4 weeks and 6 months. The high level of MYOM3 fragments were found at the both ages in MDX, KO-Sgca and KO-Sgcg mice while in KO-Dysf these fragments were barely detectable at 1 month age and reached its maximum at the age of 6 month. Only a faint labelling of MYOM3 fragment was detected in KO-Capn3 mice (FIG. 9). Interestingly, among the studied murine models of muscular dystrophies, KO-Capn3 demonstrated the weakest phenotype suggesting that the myomesin 3 serum level could correlate with the severity of the disease. In order to reinforce this hypothesis, we evaluated the level of the myomesin-3 fragments in KI-FKRP mice, a mouse model for LGMD-21. Contrary to the disease in human, mutation of the Fukutin-related protein gene in mice leads to a very mild phenotype with no myomesin 3 fragments in the serum thus confirming correlation between the severity of the dystrophy with the level of myomesin-3 fragments in serum.

Example 2

(72) In the present example, the inventors have completed their study, and show in particular that myomesin proteins are relevant tools to determine whether or not a patient carries muscular dystrophy, prediction of the development of muscular dystrophy, screening for a therapeutic agent or technique for muscular dystrophy, or for the evaluation of the efficacy of a therapeutic agent or technique for muscular dystrophy.

(73) Materials and Methods

(74) Human Sample Collection

(75) The human studies were conducted according to the principles of the declaration of Helsinki “Ethical Principles for Medical Research Involving Human Subjects”. Serum samples from a cohort of 39 young (3 to 10 years old) and 17 older (12 to 20 years old) DMD patients as well as 29 young (3 to 10 years old) and 18 older (12 to 20 years old) healthy individuals were collected at the Cincinnati Children's Hospital Medical Center USA (US cohort) as part of ADNA (Avancées Diagnostiques pour de Nouvelles Approches thérapeutiques) project (see Worldwide Website: institut-merieux.com/projetssante_adna.php). The study protocol and Informed Consent was approved by the Institutional Review Board (IRB) at Cincinnati Children's Hospital Medical Center. Informed Consent was obtained from all subjects prior to the study. The conduct of the study conforms to all applicable human subjects research regulations. Serum samples from 3 LGMD2D patients were collected at the Neuromuscular Research Center (University Hospital of Tampere, Finland) during standard day-care consultation. After collection, samples were centrifuged twice immediately (10,000×g, 10 min) and serum was stored at −80° C.

(76) Protein Quantification and Measurements of Creatine Kinase Activity

(77) Protein concentration was determined using the Bio-Rad Protein Assay Dye Reagent (Bio-Rad) according to the manufacturer's instructions with bovine serum albumin as a standard. Measurements of total creatine kinase (CK) activity were performed using the Vitros DT60 II Chemistry System according to the manufacturer's instructions (Ortho-Clinical Diagnostics).

(78) Serum Depletion

(79) Depletion of the 12 most abundant serum proteins (alpha 1-acid glycoprotein, alpha 1-antitrypsin, alpha 2-macroglobulin, albumin, apolipoprotein A-I, apolipoprotein A-II, fibrinogen, haptoglobin, IgA, IgG, IgM and transferrin) was performed with the Proteome purify 12 Human Serum Protein Immunodepletion kit (R&D Systems) according to the manufacturer's instructions with some modifications. Briefly, 1 ml of immunodepletion resin was mixed with 10 μl of pooled serum diluted with PBS to a final volume of 500 μl and incubated for 1 h at room temperature (RT). Depleted serum was collected after centrifugation (1000× g, 2 min) in Spin-X Filter Units and proteins were 5-fold concentrated using Amicon Ultra-2 Centrifugal Filter Units (cut-off 3000 kDa; Millipore) following the manufacturer's instructions.

(80) Mass Spectrometry

(81) For mass spectrometry analysis, 10 μg of depleted serum proteins were solubilised in a total of 123 μl of the reaction mixture containing 4 M urea, 1.5 M thiourea and 50 mM tris-HCl pH 8.3. Proteins were reduced with 10 mM dithiothreitol for 30 min and then alkylated with 55 mM iodoacetamide for 20 min. Alkylated proteins were first digested with 500 ng of endopeptidase lys-C (Wako) for 3 h at RT. Then, the mixture was adjusted to 235 μl with MilliQ-water and treated with 500 ng of trypsin (Sequence Grade Trypsin, Promega) for 16 h at RT. Enzymatic activity was stopped by addition of formic acid to 3% final concentration and samples were stored at −20° C. until use. The peptide mixture was desalted using ZipTip.sub.μ-C18 Pipette Tip (Millipore) and separated with an Easy nano-LC Proxeon system (Thermo Fisher Scientific) equipped with a reversed phase C18 column (Easy-Column Proxeon C18, L 10 cm, ID 75 μm). Eluates were monitored by a LTQ Velos Orbitrap mass spectrometer (Thermo Fisher Scientific) and tandem MS (MS/MS) data were processed with Proteome Discoverer 1.4 software (Thermo Fisher scientific) coupled to an in house Mascot search server (Matrix Science, 2.3.2 213 version) using SwissProt database as described previously (Rouillon et al., 2014). The relative abundance of each protein identified in serum from DMD or healthy patients was estimated by label-free quantification using the Progenesis LC-MS software (Nonlinear Dynamics, 4.0 version).

(82) Western Blot

(83) Protein samples were separated by SDS-PAGE electrophoresis (4 to 12% gradient, NuPAGE Novex Bis-Tris Gel 1.0 mm, Life Technologies) and transferred onto Protran Premium membrane (nitrocellulose, GE Healthcare). Fifty micrograms (1 μl of serum) of human, mouse, or dog serum protein were loaded per lane. Antibodies against MYOM3 (1:1000, Proteintech: 17692-1-AP) and the CK-M (1:500, Santa Cruz: sc-15161) were used as primary antibodies followed by incubation with the corresponding IRDye-800CW-conjugated antibodies (1:10,000, LI-COR Biosciences) according to the manufacturer's instructions. Infrared fluorescence of the secondary antibodies was read on an Odyssey Imaging System (LI-COR Biosciences). Band intensities were measured by the Odyssey application software (LI-COR Biosciences, Image Studio Lite 4.0 Version).

(84) Animal Experimentations

(85) Animal experimentations were conducted in accordance with the European guidelines for the protection of vertebrate animals used for experimental purposes (Directive 2010/63/EU of 22 Sep. 2010) and for the mice treated with the oligonucleotide Pip6a-PMO, in accordance to procedures authorised by the UK home office. Blood samples were collected from male dogs (provided by the CEDS at Mézilles and Oniris at Nantes, France) from the lateral saphenous vein and from mice by retro-orbital bleeding or from the jugular vein. The following mouse strains were used: C57BL/6 and C57/BL10 control strains as well as mdx (model for DMD; Chapman, 1989), and 4 knockout (KO) strains named KO-Capn3 (model for LGMD2A; Laure, et al., 2009), KO-Dysf (model for LGMD2B; Lostal, et al., 2010), KO-Sgcg (model for LGMD2C; Hack, et al., 1998) and KO-Sgca (model for LGMD2D; Duclos, et al., 1998). Blood samples were centrifuged twice (10,000× g, 10 min, 4° C.) and serum samples obtained were stored at −80° C. until use.

(86) Physical Exercise of Mice

(87) Mice were placed on a treadmill (Treadmill Exer 6M, Columbus Instruments) to run at a downward inclination of 15° at speeds of 8 m/min for 5 min, followed by 12 m/min for 25 min. Serum samples were collected by retro-orbital bleeding and stored at −80° C.

(88) Ageing in Mice

(89) Blood samples from 1-day up to 52-week-old mice (5 healthy controls or 5 mdx per age) were collected and stored at −80° C. Newborn as well as 12-, 24-, 36- and 52-week-old mice were euthanized after collection. The samples for the 1, 2, 3 and 4 week time points were collected from the same group of mice.

(90) Antisense Oligonucleotide-Mediated Exon Skipping Therapy of mdx Mice

(91) Twelve-week-old mdx mice were treated with a single 12.5 mg/kg tail vein injection of an arginine-rich cell-penetrating peptide conjugated to a phosphorodiamidate morpholino oligonucleotide, Pip6a-PMO (peptide RXRRBRRXRYQMRXRBRXRB coupled through an amide linkage at the 3′ of the oligonucleotide 5′-GGCCAAACCTCGGCTTACCTGAAAT-3′)(SEQ ID NO: 25), synthesised and prepared in a sterile saline solution as described previously (Betts et al, 2012; Roberts et al, 2012). Blood samples were collected prior and 2, 4 and 8 weeks post-injection and the serum levels of the MYOM3 fragments and CK-M were monitored by Western blot analysis.

(92) Gene Therapy Treatment of KO-Sgca Mice

(93) Recombinant adeno-associated virus 8 (rAAV2/8) vector was used to restore α-sarcoglycan expression in KO-Sgca mice. The production of rAAV was performed by dual infection of Sf9 cells with baculoviruses harbouring cDNA for Sgca under the desmin promoter and regulated by miR-142-3p (Boisgerault et al, 2013) and AAV rep2/cap8 genes (rAAV2/8). The purification was performed on immuno-affinity AVB SEPHAROSE medium (GE Healthcare) according to (Smith et al, 2009). Four groups of 5 week old KO-Sgca mice (5 mice per group, except 4 mice for the highest vector dose) were injected either with PBS or with increasing doses of rAAV (1e11, 5e11, and 1e12 viral genome (vg)). Blood samples were collected biweekly for 3 months and levels of the MYOM3 fragments and CK were monitored by Western blot analysis and measurements of CK activity, respectively. Muscle force was measured by the escape test 1 week before sacrifice. Restoration of the sarcoglycan complex and muscle morphology were assessed by immunostaining and histological analyses.

(94) Evaluation of Muscle Force in Mice

(95) Mouse muscle force was evaluated by the whole body tension method or escape test (Carlson & Makiejus, 1990) with some modifications. Mice attached to the tail with a thread connected to a tension transducer were placed on a platform facing the entrance of a 30 cm long tube. In response to pinching of the tail, mice try to escape within the tube thus raising a short peak of force (forward pulling tension, FPT) that is recorded. Five FPTs were recorded for each mouse. The body weight of each mouse was measured and the WBT was obtained by dividing the average of the 5 FPTs with the body weight.

(96) Statistical Analysis

(97) Statistical analyses were performed using the GraphPad Prism version 6.04. Data are expressed as mean±SD if not otherwise specified. For comparisons between means, homogeneity of variances was assessed by Fisher-Snedecor's test and the Student's t-test (two-tailed) was applied. Pearson's correlation was used for correlation studies and data were analyzed with a 95% confidence interval and P<0.05 was considered significant.

(98) Histology and Sgca Immunostaining

(99) Cryosections (8 mm thickness) were prepared from frozen right and left gastrocnemius muscles. Transverse sections were processed for hematoxylin phloxine saffron (HPS) histological staining. Colorimetric immunodetection of Sgca was performed as previously described (Fougerousse et al, 2007).

(100) After digitization of immunostained biopsies (Axioscan, ZEISS) the total surface of the biopsies and the surface stained for α-sarcoglycan were quantified using the Image) software (version 1.47g 64-hits, Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda, Md., USA, see Worldwide Website: imagej.nih.gov/ij/, 1997-2014) and a customized script (available on demand). The percentage of Sgca positive fibres for a given biopsy was calculated using the following equation: (number of Sgca positive pixels on the biopsy area/surface in μm.sup.2 of the biopsy area) divided by the same ratio obtained for healthy control (number of Sgca positive pixels on the biopsy area/surface in μm.sup.2 of the biopsy of the control C57BL/6J mouse) and multiplied by 100.

(101) Results

(102) Detection of Differentially Expressed Serum Proteins in DMD Patients by Mass Spectrometry

(103) Serum samples from 39 patients and 38 control subjects collected in USA as part of the ADNA project (see Worldwide Website: institut-merieux.com/projetssante_adna.php) (the entire US cohort comprised 103 patients and control subjects) were analysed using a mass spectrometry approach. To reduce the number of LC-MS/MS analyses, the samples were organised into 4 groups (G1: young DMD from 3 to 10 years old; G2: older DMD from 12 to 20 years old; G3: young controls from 3 to 10 years old; and G4: older controls from 12 to 20 years old) subdivided in a total of 12 pools according to the patient's age (Table 2). Each pool included sera from at least 4 individuals where serum of each individual was equally represented. In order to ensure deep proteome coverage, the pools were immunodepleted for the 12 major serum proteins.

(104) TABLE-US-00002 TABLE 2 List of differentially expressed proteins between G1 and G3 groups (young DMD and age matched healthy controls) classified by the decrease in the ratio DMD/healthy (fold change). Top 10 proteins with the lowest p-value are in bold. All shown proteins passed thresholds of peptide numbers ≥2, a score ≥50, a fold change ≥2 and a p-value ≤0.05. Peptides: number of peptides identified for a given protein. Score: Mascot protein score. ANOVA Fold No. accession Description Localization Peptides Score (p-value) change MYG_HUMAN Myoglobin Cytoplasm 4 195 2.7e−03 234.8 MYOM2_HUMAN MYOM2 Myofibril 10 390 9.8e−05 100.1 MYOM3_HUMAN MYOM3 Myofibril 11 491 1.5e−05 49.7 TPIS_HUMAN Triosephosphate Cytoplasm 3 128 2.3e−03 48.4 isomerase AATC_HUMAN Aspartate Cytoplasm 3 75 4.7e−04 45.7 aminotransferase KCRM_HUMAN CK-M Cytoplasm 15 849 2.9e−05 39.8 MYH7_HUMAN Myosin-7 Myofibril 11 520 2.2e−05 38.3 ENOB_HUMAN β-enolase Cytoplasm 4 178 7.4e−05 34.8 G6PI_HUMAN Glucose-6-phosphate Cytoplasm/ 4 130 1.6e−03 29.5 isomerase Secreted CAH3_HUMAN Carbonic anhydrase 3 Cytoplasm 5 182 8.6e−05 23.9 FLNC_HUMAN Filamin-C Myofibril 4 145 4.3e−04 19.4 ALAT1_HUMAN Alanine Cytoplasm 4 127 3.0e−05 15.6 aminotransferase 1 ALDOA_HUMAN Fructose- Cytoplasm 15 729 9.3e−05 14.2 bisphosphate aldolase A KPYM_HUMAN Pyruvate kinase PKM Cytoplasm 16 845 1.1e−05 12.8 TITIN_HUMAN Titin Myofibril 14 495 1.9e−03 10.8 VINC_HUMAN Vinculin Cytoplasm/Membrane 2 74 7.2e−05 10.3 PYGM_HUMAN Glycogen Cytoplasm 8 257 6.1e−04 9.9 phosphorylase, muscle form LDHA_HUMAN L-lactate Cytoplasm 8 378 9.1e−04 9.5 dehydrogenase A chain HPT_HUMAN Haptoglobin Secreted 29 1867 1.5e−04 7.6 HBD_HUMAN Hemoglobin subunit δ Cytoplasm 3 100 5.1e−03 6.2 LDHB_HUMAN L-lactate Cytoplasm 10 598 2.4e−05 5.4 dehydrogenase B HBB_HUMAN Hemoglobin subunit β Cytoplasm 7 552 8.0e−03 3.6 HBA_HUMAN Hemoglobin subunit α Cytoplasm 7 407 5.3e−03 3.4 TPM2_HUMAN Tropomyosin βchain Myofibril 5 170 2.0e−02 2.6 VASN_HUMAN Vasorin Membrane 4 135 4.0e−02 0.5 ALS_HUMAN Insulin-like growth Secreted 22 1096 1.0e−02 0.5 factor-binding protein complex PHLD_HUMAN Phosphatidylinositol- Secreted 9 533 4.7e−03 0.5 glycan-specific phospholipase D CHL1_HUMAN Neural cell adhesion Membrane/ 2 66 3.0e−02 0.5 molecule L1-like Secreted protein COL11_HUMAN Collectin-11 Secreted 2 72 2.6e−03 0.4 CADH5_HUMAN Cadherin-5 Membrane 6 220 2.0e−03 0.4 CD109_HUMAN CD109 antigen Membrane 2 59 3.0e−02 0.4 LBP_HUMAN Lipopolysaccharide- Secreted 7 386 5.0e−03 0.4 binding protein CRAC1_HUMAN Cartilage acidic protein 1 Secreted 6 223 2.0e−02 0.4 C4BPB_HUMAN C4b-binding protein Secreted 4 207 2.0e−02 0.4 CNDP1_HUMAN β-Ala-His dipeptidase Secreted 8 294 4.2e−03 0.3 DPP4_HUMAN Dipeptidyl peptidase 4 Membrane/ 5 162 5.5e−03 0.3 Secreted CETP_HUMAN Cholesteryl ester Secreted 7 296 8.2e−04 0.2 transfer protein

(105) Mass spectrometry analysis of serum samples of all 12 subgroups enabled the identification a total of 3329 unique peptides matching 378 proteins (with a false discovery rate less than 0.01). Among those, 69% of protein identification calls (260 proteins) were based on spectra from 2 or more peptides. To reveal proteins differentially present in sera from DMD and healthy individuals, the data were analysed by a label-free quantification approach using the following parameters: number of peptides ≥2; protein score ≥50 and fold change ≥2. The analysis of G1 versus G3 groups revealed 24 proteins more abundant in DMD and 13 in healthy subjects (Table 3). The top 10 proteins with the lowest p-value were overexpressed in DMD patients and either involved in muscle energy metabolism (pyruvate kinase PKM, L-lactate dehydrogenase B chain, CK-M, alanine aminotransferase 1, β-enolase, carbonic anhydrase 3, fructose-bisphosphate aldolase A), in sarcomere organisation (myomesin-3, myosin-7) or costamere organisation (vinculin).

(106) TABLE-US-00003 TABLE 3 List of differentially expressed proteins in serum samples between G2 and G4 groups (older DMD and age matched healthy controls) classified by the decrease in the ratio DMD/healthy (fold change). All shown proteins passed thresholds of peptide numbers ≥2, a score ≥50, a fold change ≥2 and a p-value ≤0.05. Peptides: number of peptides identified for a given protein. Score: Mascot protein score. ANOVA Fold No. accession Description Localization peptides Score (p-value) change KCRM_HUMAN CK-M Cytoplasm 3 96 1.0e−02 19.5 ADIPO_HUMAN Adiponectin Secreted 3 213 3.0e−02 4.4 ALDOA_HUMAN Fructose-bisphosphate Cytoplasm 2 84 3.0e−02 3.3 aldolase A HBB_HUMAN Hemoglobin subunit β Cytoplasm 9 632 8.4e−03 2.4 LDHB_HUMAN L-lactate Cytoplasm 6 223 4.0e−02 2.2 dehydrogenase B chain GELS_HUMAN Gelsolin Cytoplasm 32 2287 1.0e−02 0.5 LCAT_HUMAN Phosphatidylcholine- Secreted 6 295 1.0e−02 0.4 sterol acyltransferase CAD13_HUMAN Cadherin-13 Membrane 2 86 5.8e−03 0.4 CRAC1_HUMAN Cartilage acidic Secreted 3 105 1.0e−02 0.2 protein 1

(107) Comparison of older DMD patients with their age matched controls (G2 versus G4) using the same parameters resulted in only 9 differentially expressed proteins: 5 proteins more abundant in DMD (CK-M, adiponectin, fructose-bisphosphate aldolase A, L-lactate dehydrogenase B chain, and hemoglobin β) and 4 in healthy subjects (gelsolin, phosphatidylcholine-sterol acyltransferase, cadherin-13, cartilage acidic protein 1) (Table 3). Only 4 of these proteins (CK-M, fructose-bisphosphate aldolase A, L-lactate dehydrogenase B chain and hemoglobin β) were differentially abundant in both DMD age groups according to the mass spectrometry analysis. Importantly, the expression ratios for these four proteins in DMD versus healthy controls were substantially lower in older DMD patients as compared to the young DMD group (19.5; 3.3; 2.2 and 2.4 folds in older DMD versus 39.8; 14.2; 5.4 and 3.6 times in young, respectively). The decrease in the number of differentially expressed proteins and in magnitude of their fold changes is most probably due to the drastic decrease of muscle mass in older DMD patients (12-20 years old), and relative immobility of these patients. Interestingly, label-free analysis of young and older DMD patients (G1 versus G2) revealed 8 secreted proteins that increased in abundance with patient age (dopamine β-hydroxylase: 3 fold, adiponectin: 3 fold, serum amyloid P-component: 3 fold, insulin-like growth factor-binding protein complex acid labile subunit: 3 fold, β-Ala-His dipeptidase: 5 fold, insulin-like growth factor I: 5 fold).

(108) Levels of MYOM3 Demonstrate Less Inter-Individual Variations Compared to CK in DMD Patients

(109) Elevated levels of cytosolic myofibrillar proteins such as CK in the blood are now widely used as the first stage of DMD diagnosis (Gasper & Gilchrist, 2005; Moat et al, 2013). Therefore, it was appealing to compare serum levels of CK with one of the myofibrillar structural proteins found in the present study. Based on the high fold change (50) and low p-value (1.5e-5) between DMD and healthy controls (Table 2), MYOM3 protein (UniProtKB #Q5VTT5) was chosen for further analysis. MYOM3, a protein of 1437 amino acids (162.2 kDa), is a member of a family of closely related structural proteins detected at the M-band of the sarcomere in striated skeletal muscles: MYOM1, MYOM2 (or M protein) and MYOM3. These proteins are involved in sarcomere stability and resistance during intense or sustained stretching (Schoenauer et al., 2008). Detailed analysis of MS/MS data showed that the 25 identified peptides were equally distributed along the MYOM3 sequence indicating that the entire protein (or fragments covering the entire length of the protein) was present in serum.

(110) As mentioned in example 1, western blot analysis of serum from DMD patients with an anti-MYOM3 antibody targeting the last 325 amino acids at the C-terminus revealed the presence of two bands of 100 and 140 kDa respectively (FIG. 11). Given that intact MYOM3 has a predicted size of 162 kDa, this suggests that these two bands correspond to C-terminal fragments of the protein. Importantly, fragments of the same size were barely detectable in sera from healthy subjects, thus validating the mass spectrometry data.

(111) We next compared the levels of the MYOM3 fragments and CK in all 103 subjects from the US cohort. The serum expression levels of both MYOM3 fragments were determined by Western blot analysis and CK assessed by measuring its enzymatic activity (FIG. 12). In accordance with the mass spectrometry data, results showed that expression levels of both, CK and the MYOM3 fragments, were much higher in young DMD patients compared to the respective healthy controls (ratio DMD/Control: CK=193 and MYOM3=185) (FIGS. 12A and 12B). In older DMD patients, the expression levels of CK and MYOM3 fragments were respectively 14 and 5 times lower than in young DMD patients.

(112) Importantly, even if both proteins were able to discriminate DMD patients and healthy controls, there were less inter-individual variations in MYOM3 fragment levels compared to CK levels. While the CK levels in the young patients varied from 9000 IU/L to 60 000 IU/L (mean 27130 IU/L±13130), the values for MYOM3 fragments remained between 11 a.u. and 24 a.u. (mean 19 a.u.±3). The low correlation observed between the levels of serum CK and MYOM3 fragments in the group of young patients (R.sup.2=0.28) indicates that different physiological mechanisms may account for the secretion/stability of these proteins at this age. (FIG. 12C). Conversely, these two biomarkers were well correlated in older patients (FIG. 12D).

(113) MYOM3 Fragments are Specifically Present in Sera from Animal Models of DMD.

(114) The levels of MYOM3 fragments were quantified in two animal models of DMD: Golden Retriever muscular dystrophy (GRMD) which has a severe phenotype similar to DMD patients (Kornegay et al, 2012) and dystrophin-deficient mdx mice. Western blot analysis of GRMD and mdx sera revealed the presence of 2 bands migrating at the same positions as human MYOM3 fragments. Importantly, the abundance of these fragments was 100 times higher than in the healthy control dogs (FIGS. 13A, B). Whereas the level of the MYOM3 fragments in human DMD samples decreased with age, expression of these fragments was very similar in the serum of 2 and 18 month old GRMD (GRMD dogs usually do not survive beyond this age without special care). Age-independent expression of the MYOM3 fragments could be an advantage for utilisation of this biomarker in gene therapy studies conducted in dogs.

(115) MYOM3 Fragments are Specifically Expressed in Sera of LGMD2D Patients and Mouse Models of LGMDs.

(116) The presence of the MYOM3 fragments was also analysed in serum samples of 3 patients with α-sarcoglycanopathy (LGMD2D). Fragments of the same length (100 and 140 kDa) were detected at elevated levels in all these patients. Overall, the level of these fragments in LGMD2D patients was lower compared to their intensity in young DMD patients (FIG. 14A). The following mouse models of limb girdle muscular dystrophies were included in this study: KO-Calpain 3 (models for LGMD2A) (Richard et al, 2000), KO-Dysferlin (models for LGMD2B) (Lostal et al, 2010), KO-Sgcg (models for LGMD2C) (Hack et al, 1998), and KO-Sgca (models for LGMD2D) (Duclos et al, 1998). These mouse models are congenic strains on the genetic background of the C57BL/6J mouse, which was included in the study as their wild type (WT) control. Taking into consideration the muscle impairment and time of disease onset, these mouse models can be classified in terms of decreasing order of severity: KO-Sgca, KO-Sgcg, KO-dysf and KO-Capn3. Serum from these mouse models was collected at 1 and 6 months of age, corresponding to the early and advanced stages of the dystrophies, and the levels of the MYOM3 fragments were compared by Western blot. The highest levels of serum MYOM3 fragments were observed in the three mouse models with perturbations in the DAPC (FIG. 14B). In KO-Dysf mice, these fragments were barely detectable at 1 month of age and then increased at 6 months, reflecting the aggravation of the disease at this age. MYOM3 fragments were hardly detectable in KO-Capn3 mice at any age.

(117) In Mdx Mice, the MYOM3 Fragments are Expressed Early, Demonstrate Less Inter-Individual Variability and are Less Sensitive to Physical Exercise Compared to CK.

(118) In order to identify the earliest time point when the serum MYOM3 fragments are detectable, we investigated sera from mdx mice of different ages (from birth to 1 year old). The MYOM3 fragments were detected in mdx mice at birth, with a small decrease in their levels at 1 week of age and followed by a rise in abundance at 3 weeks (FIG. 15A). Importantly, the levels of these fragments in the age-matched control mice was lower at all ages tested (FIG. 15B). The kinetics of the MYOM3 fragment abundance in the serum of mdx mice correlates with the timing of an acute phase of muscle necrosis generally occurring at 3 to 4 weeks of age, followed by an apparent stabilisation of the muscle phenotype (Cullen & Jaros, 1988). The kinetics of serum CK levels in mdx mice were different from that of the MYOM3 fragments during the first weeks of age. Consistent with previous studies (McArdle et al, 1994; Wooddell et al, 2010) serum CK was elevated in newborn mice, but then became undetectable during the 1st and 2nd week of age (except for 1 mouse), rising again at 3 and 12 weeks followed by a stabilisation (FIG. 15C). In healthy mice serum CK was also slightly elevated in newborns and 12- and 24-week-old animals (FIG. 15D). Importantly, less variation was observed in the levels of MYOM3 fragments in mice of the same age compared to the CK (maximum fold change 2 for MYOM3 versus 110 for CK). The difference in age-dependent expression patterns between serum CK and MYOM3 fragments in mdx mice is probably related to different mechanisms of bioprocessing of these proteins, especially during the early phases of disease.

(119) To assess the impact of physical exercise on the serum levels of the MYOM3 fragments and CK, WT and mdx mice were subjected to downhill running for 30 min. This exercise regimen is often used to increase muscle injury and worsen the mdx phenotype (Brussee et al, 1997; Vilquin et al, 1998). Sera were collected 7 days before and 3, 24 and 48 hours after exercise. Importantly, while in mdx mice CK concentration peaked at 3 hours post-exercise (up to 10 fold increase) followed by a substantial decrease (FIG. 16C), physical exercise had relatively little impact on the serum levels of the MYOM3 fragments (less than 2 fold increase 48 h post-exercise) (FIG. 16A). Interestingly, in healthy mice, there was a slight increase in the levels of the MYOM3 fragments 24 and 48 h after exercise, even though the maximum level of the fragments in healthy mice was 50 fold less than in mdx mice (FIG. 16B). Serum CK levels were variable in healthy mice without noticeable correlation with physical exercise (FIG. 16D). Given that MYOM3 is predominantly expressed in slow and intermediate speed (type I and IIa) skeletal fibres (Schoenauer et al, 2008) which are less affected in DMD relative to fast myofibres (Webster et al, 1988), it is possible that the difference in the kinetics of these biomarkers is partially due to the differential sensitivity of these muscle fibre types to exercise-induced damage.

(120) MYOM3 Fragments Enable Monitoring of Pharmaco- and Gene Therapy Treatment Efficacy.

(121) The presence of the MYOM3 fragments in serum of DMD and LGMD2D patients and their respective mouse models prompted us to evaluate the utility of these biomarkers for monitoring the response to experimental therapies in mdx and KO-Sgca mice.

(122) Restoration of dystrophin expression in mdx mouse muscles was achieved by a single administration of an arginine-rich cell-penetrating peptide (CPP) conjugated to a phosphorodiamidate morpholino oligonucleotide (PMO) that efficiently induces skipping of exon 23 and restores dystrophin protein expression and muscle function (Betts et al, 2012; Yin et al, 2011). In order to evaluate the impact of the restoration of dystrophin expression on the serum levels of MYOM3 fragments and CK, blood samples from treated mdx, non-treated mdx and WT control mice were collected 2, 4 and 8 weeks post-injection. Two weeks after injection, the levels of the MYOM3 fragments in treated mdx mice substantially decreased (without reaching the level in the control mice) and then gradually increased over time (FIG. 7A). These data are in a good agreement with the restoration of the dystrophin expression observed in 30 to 60% of muscle fibres 2 weeks after injections (Betts et al, 2012; Yin et al, 2011), followed by a decrease in the percentage of positive fibres at later time points (Jearawiriyapaisarn et al, 2010). In contrast to the MYOM3 fragments, CK levels did not reflect restoration of dystrophin expression. Thus, 2 weeks after injection the level of serum CK was lower in treated mdx mice compared to WT control mice (FIG. 17B), while dystrophin expression did not exceed 60% at that time. Moreover, 8 weeks after the treatment, when the estimated level of dystrophin-positive fibres was around 20% (Betts et al, 2012; Yin et al, 2011), CK levels were higher in treated than in non-treated mdx mice. Different behaviour of the MYOM3 fragments and CK after partial restoration of dystrophin expression may reflect the capacity of these biomarkers to differentially reveal intracellular process such as microparticle turnover (Duguez et al, 2013) or increased myofibrillar protein catabolism (McKeran et al, 1977; Mussini et al, 1984).

(123) To restore α-sarcoglycan expression in KO-Sgca mice, we used recombinant adeno-associated virus rAAV2/8 vector. Control C57BL/6J mice received an intravenous injection of PBS and four groups of KO-Sgca mice received intravenous injections of either PBS or low (1e11 vg), medium (5e11 vg) or high (1e12 vg) doses of rAAV2/8 coding for hSGCA. Mice were monitored for three months after the treatment. The following assays were compared in order to define the most appropriate for the follow up of the treatment: histological analysis of muscle biopsies (HPS staining and restoration of the sarcoglycan complex); total physical force 3 months after the treatment (1 week before animal sacrifice); biweekly analysis of serum CK and MYOM3 fragments levels.

(124) Histological analysis of the gastrocnemius muscles demonstrated restoration of the complex in 5-30% (mean 15.6±8.4), 60-100% (mean 79.2±16.7), and 84-100% (mean 94.6±8.8) of fibres after low, medium and high rAAV dose treatments, respectively (FIGS. 18A, B). Importantly, by assessing the expression level of α-sarcoglycan (determined by immunostaining) the KO-Sgca, low, medium and WT mice could be clearly distinguished. However, no statistically significant difference was found between medium and high rAAV doses by this method. Importantly, this analysis is highly laborious, and the size of the biopsies makes it unsuitable for the follow-up of the therapeutic effect in small animals.

(125) Similar to histological analysis, the conventional whole body tension method (WBT) is an end-point assay because mice become accustomed to the protocol (Carlson et al, 2010). The WBT method was only able to discriminate 2 clusters of animals: (1) KO-Sgca mice injected with PBS or low dose of rAAV and (2) control C57BL/6J mice and KO-Sgca mice injected with medium or high doses of rAAV (FIG. 18C).

(126) A threshold 3000 IU/L of CK clearly separates KO-Sgca mice injected with PBS from all other experimental groups (FIGS. 18D, F). Nevertheless, when applying the Student's test (P-value threshold <0.01), differences only between few time points/injection doses appeared as statistically significant (FIG. 18F). Changing of the p-value threshold to <0.05 permits to distinguish more experimental groups of mice (FIG. 18F). Lower CK levels in all groups of mice at day 90 (one week after the total force measurements) (FIG. 18D) could be explained by the fact that an increase of CK levels after physical exertion is followed by a substantial decrease persisting for 2 weeks (Kobayashi et al, 2012).

(127) Inter-individual variations of the MYOM3 fragment levels were lower compared to serum CK in the case of all experimental groups (FIGS. 18D, E). In accordance with a previous study showing progressive development of muscular dystrophy in KO-Sgca mice (Duclos et al, 1998) the levels of the MYOM3 fragments in the control mice injected with PBS increased gradually with age (FIG. 18E). Even the lowest dose of rAAV (1e11 vg) stabilised the MYOM3 fragment levels, while medium and high doses reduced MYOM3 fragment levels 5 fold and 8 fold, respectively. Due to the low inter-individual variability, measurement of the MYOM3 fragments enabled nearly all groups of mice to be distinguished with either of the thresholds (P-values <0.01 or 0.05) at the majority of time points (FIGS. 18E, F). Furthermore, MYOM3 fragment abundance was better correlated (R.sup.2=0.71) with muscle force as measured by the escape test compared with CK (R.sup.2=0.59) (FIG. 19).

(128) Comparison of MYOM3 fragments with 3 other assays (biopsy, restoration of physical force, and CK) in models of 2 different muscular dystrophies, mdx (dystrophin deficient) and KO-Sgca (α-sarcoglycan deficient), demonstrated the superiority of MYOM3 fragments for the follow-up of gene therapy treatments relative to other assays. The advantages of the MYOM3 fragments compared to CK are their lower inter-individual variability between the patients of the same age, better correlation with the reconstitution of the dystrophin associated protein complex and muscle force restoration. The critical advantages of the MYOM3 fragments compared to the histological analysis of biopsies are that they are less invasive and provide information concerning body-wide muscle integrity. MYOM3 was the most efficient biomarker for distinguishing the 5 groups of KO-Sgca mice treated with different doses of rAAV vector. Taken together, our data demonstrate that MYOM3 fragments are excellent biomarkers for monitoring therapeutic outcomes in DMD and other muscular dystrophy patients.

(129) Differential Expression of Different Myomesin Proteins May be Monitored to Study the Status of Different Types of Muscle Fibres.

(130) Differential expression of different myomesins in muscle fibres (MYOM3 was found mainly in intermediate speed fibres (type IIa) of skeletal muscle, while fast fibres express more MYOM2 and MYOM1 is expressed in all muscle fibres (Schoenauer et al, 2008)) implies a possibility to follow the results of therapeutic treatment for each type of muscle fibres. We have found that after physical exercises fragments of myom2 and myom3 appeared in the bloodstream of mdx mice at different time, peaking at 1 and 2 days after exercise respectively (FIG. 21 and FIG. 16). This corresponds to the fact that fast muscles, rich in myom2, are preferentially affected in Duchenne muscular dystrophy (Webster, 1988).

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