Mass spectrometry-based proteomics: a useful tool for biomarker discovery?

A biomarker is defined as a biological substance (i.e., protein, metabolite, specific post-translational modification) that can be used to detect a disease, measure its progression or the effects of a treatment. Importantly, a biomarker should be readily accessible (i.e., present within body fluids); it must also provide sufficient sensitivity and specificity to accurately distinguish between true positives, false positives, and false negatives. Even more importantly, detection of the biomarker should provide clinical benefits to the patient (i.e., improved survival and/or quality of life). Due to recent technical advances in biomolecular mass spectrometry, a great deal of effort has gone into the discovery of biomarkers at an international level. In this commentary we set forth our views on how mass spectrometry (MS) could be applied to the discovery of elusive biomarkers (Figure 1).

Increased expression of utrophin in a slow vs. a fast muscle involves posttranscriptional events.

In addition to showing differences in the levels of contractile proteins and metabolic enzymes, fast and slow muscles also differ in their expression profile of structural and synaptic proteins. Because utrophin is a structural protein expressed at the neuromuscular junction, we hypothesize that its expression may be different between fast and slow muscles. Western blots showed that, compared with fast extensor digitorum longus (EDL) muscles, slow soleus muscles contain significantly more utrophin. Quantitative RT-PCR revealed that this difference is accompanied by a parallel increase in the expression of utrophin transcripts. Interestingly, the higher levels of utrophin and its mRNA appear to occur in extrasynaptic regions of muscle fibers as shown by immunofluorescence and in situ hybridization experiments. Furthermore, nuclear run-on assays showed that the rate of transcription of the utrophin gene was nearly identical between EDL and soleus muscles, indicating that increased mRNA stability accounts for the higher levels of utrophin in slow muscles. Direct plasmid injections of reporter gene constructs showed that cis-acting elements contained within the utrophin 3'-untranslated region (3'-UTR) confer greater stability to chimeric LacZ transcripts in soleus muscles. Finally, we observed a clear difference between EDL and soleus muscles in the abundance of RNA-binding proteins interacting with the utrophin 3'-UTR. Together, these findings highlight the contribution of posttranscriptional events in regulating the expression of utrophin in muscle.

Distinct regions in the 3' untranslated region are responsible for targeting and stabilizing utrophin transcripts in skeletal muscle cells.

In this study, we have sought to determine whether utrophin transcripts are targeted to a distinct subcellular compartment in skeletal muscle cells, and have examined the role of the 3' untranslated region (UTR) in regulating the stability and localization of utrophin transcripts. Our results show that utrophin transcripts associate preferentially with cytoskeleton-bound polysomes via actin microfilaments. Because this association is not evident in myoblasts, our findings also indicate that the localization of utrophin transcripts with cytoskeleton-bound polysomes is under developmental influences. Transfection of LacZ reporter constructs containing the utrophin 3'UTR showed that this region is critical for targeting chimeric mRNAs to cytoskeleton-bound polysomes and controlling transcript stability. Deletion studies resulted in the identification of distinct regions within the 3'UTR responsible for targeting and stabilizing utrophin mRNAs. Together, these results illustrate the contribution of posttranscriptional events in the regulation of utrophin in skeletal muscle. Accordingly, these findings provide novel targets, in addition to transcriptional events, for which pharmacological interventions may be envisaged to ultimately increase the endogenous levels of utrophin in skeletal muscle fibers from Duchenne muscular dystrophy (DMD) patients.

A novel mechanism for modulating synaptic gene expression: differential localization of alpha-dystrobrevin transcripts in skeletal muscle.

Alpha-dystrobrevin is a dystrophin-related and -associated protein that is involved in synapse maturation and is required for normal muscle function. There are three protein isoforms in skeletal muscle, alpha-dystrobrevin-1, -2, and -3 that are encoded by the single alpha-dystrobrevin gene. To understand the role of these proteins in muscle we have investigated the localisation and transcript distribution of the different alpha-dystrobrevin isoforms. Alpha-dystrobrevin-1 and -2 are concentrated at the neuromuscular junction and are both recruited into agrin-induced acetylcholine receptor clusters in cultured myotubes. We also demonstrate that all alpha-dystrobrevin mRNAs are transcribed from a single promoter in skeletal muscle. However, only transcripts encoding alpha-dystrobrevin-1 are preferentially accumulated at postsynaptic sites. These data suggest that the synaptic accumulation of alpha-dystrobrevin-1 mRNA occurs posttranscriptionally, identifying a novel mechanism for synaptic gene expression. Taken together, these results indicate that different isoforms possess distinct roles in synapse formation and possibly in the pathogenesis of muscular dystrophy.

Regulation and functional significance of utrophin expression at the mammalian neuromuscular synapse.

Duchenne muscular dystrophy (DMD) is caused by the absence of full-length dystrophin molecules in skeletal muscle fibers. In normal muscle, dystrophin is found along the length of the sarcolemma where it links the intracellular actin cytoskeleton to the extracellular matrix, via the dystrophin-associated protein (DAP) complex. Several years ago, an autosomal homologue to dystrophin, termed utrophin, was identified and shown to be expressed in a variety of tissues, including skeletal muscle. However, in contrast to the localization of dystrophin in extrajunctional regions of muscle fibers, utrophin preferentially accumulates at the postsynaptic membrane of the neuromuscular junction in both normal and DMD adult muscle fibers. Since it has recently been suggested that the upregulation of utrophin might functionally compensate for the lack of dystrophin in DMD, considerable interest is now directed toward the elucidation of the various regulatory mechanisms presiding over expression of utrophin in normal and dystrophic skeletal muscle fibers. In this review, we discuss some of the most recent data relevant to our understanding of the impact of myogenic differentiation and innervation on the expression and localization of utrophin in skeletal muscle fibers.

Expression of the utrophin gene during myogenic differentiation.

The process of myogenic differentiation is known to be accompanied by large increases ( approximately 10-fold) in the expression of genes encoding cytoskeletal and membrane proteins including dystrophin and the acetylcholine receptor (AChR) subunits, via the effects of transcription factors belonging to the MyoD family. Since in skeletal muscle (i) utrophin is a synaptic homolog to dystrophin, and (ii) the utrophin promoter contains an E-box, we examined, in the present study, expression of the utrophin gene during myogenic differentiation using the mouse C2 muscle cell line. We observed that in comparison to myoblasts, the levels of utrophin and its transcript were approximately 2-fold higher in differentiated myotubes. In order to address whether a greater rate of transcription contributed to the elevated levels of utrophin transcripts, we performed nuclear run-on assays. In these studies we determined that the rate of transcription of the utrophin gene was approximately 2-fold greater in myotubes as compared to myoblasts. Finally, we examined the stability of utrophin mRNAs in muscle cultures by two separate methods: following transcription blockade with actinomycin D and by pulse-chase experiments. Under these conditions, we determined that the half-life of utrophin mRNAs in myoblasts was approximately 20 h and that it remained largely unaffected during myogenic differentiation. Altogether, these results show that in comparison to other synaptic proteins and to dystrophin, expression of the utrophin gene is only moderately increased during myogenic differentiation.

Discordant expression of utrophin and its transcript in human and mouse skeletal muscles.

In order to determine the mechanisms regulating utrophin expression in human skeletal muscle, we examined the expression and distribution of utrophin and its transcript in biopsies from normal subjects as well as from Duchenne muscular dystrophy (DMD) and polymyositis (PM) patients. We first determined by immunoblotting that in comparison to biopsies from normal subjects, utrophin levels were indeed higher in muscle samples from both DMD and PM patients as previously shown. By contrast, levels of utrophin mRNAs as determined by both RT-PCR assays and in situ hybridization, were identical in muscle samples obtained from normal subjects versus DMD and PM patients. In these experiments, we also noted that while utrophin transcripts had a clear tendency to accumulate within the postsynaptic sarcoplasm of normal human muscle fibers, the extent of synaptic accumulation was considerably less than that which we recently observed in mouse muscle fibers. The distribution of utrophin transcripts in synaptic and extrasynaptic compartments of muscle fibers obtained from DMD and PM patients was similar to that seen along muscle fibers from normal subjects. Finally, we also monitored expression of utrophin and its transcripts during regeneration of mouse muscle induced to degenerate by cardiotoxin injections. In these regenerating muscles, we observed by both immunoblotting and immunofluorescence, a large increase (4- to 7-fold) in the levels of utrophin. In agreement with our results obtained with human muscle, the increase in utrophin levels in regenerating mouse muscle was not accompanied by parallel changes in the abundance of utrophin transcripts. Taken together, these results indicate that the levels of utrophin and its transcript in muscle are discordantly regulated under certain conditions thereby highlighting the important contribution of post-transcriptional regulatory mechanisms in the control of utrophin levels in skeletal muscle fibers.

Induction of utrophin gene expression by heregulin in skeletal muscle cells: role of the N-box motif and GA binding protein.

The modulation of utrophin gene expression in muscle by the nerve-derived factor agrin plausibly involves the trophic factor ARIA/heregulin. Here we show that heregulin treatment of mouse and human cultured myotubes caused a approximately 2.5-fold increase in utrophin mRNA levels. Transient transfection experiments with utrophin promoter-reporter gene constructs showed that this increase resulted from an enhanced transcription of the utrophin gene. In the case of the nicotinic acetylcholine receptor delta and epsilon subunit genes, heregulin was previously reported to stimulate transcription via a conserved promoter element, the N-box, which binds the multimeric Ets-related transcription factor GA binding protein (GABP). Accordingly, site-directed mutagenesis of a single N-box motif in the utrophin gene promoter abolished the transcriptional response to heregulin. In addition, overexpression of heregulin, or of the two GABP subunits in cultured myotubes, caused an N-box-dependent increase of the utrophin promoter activity. In vivo, direct gene transfer into muscle confirmed that heregulin regulates utrophin gene expression. Finally, electrophoretic mobility shift assays and supershift experiments performed with muscle extracts revealed that the N-box of the utrophin promoter binds GABP. These findings suggest that the subsynaptic activation of transcription by heregulin via the N-box motif and GABP are conserved among genes expressed at the neuromuscular junction. Because utrophin can functionally compensate for the lack of dystrophin, the elucidation of the molecular mechanisms regulating utrophin gene transcription may ultimately lead to therapies based on utrophin expression throughout the muscle fibers of Duchenne muscular dystrophy patients.

Molecular mechanisms and putative signalling events controlling utrophin expression in mammalian skeletal muscle fibres.

The absence of full-length dystrophin molecules in skeletal muscle fibres results in the most severe form of muscular dystrophy, the Duchenne form (DMD). Several years ago, an autosomal homologue to dystrophin, termed utrophin, was identified. Although utrophin is expressed along the sarcolemma in developing, regenerating and DMD muscles, it nonetheless accumulates at the postsynaptic membrane of the neuromuscular junction in both normal and DMD adult muscle fibres. Due to the high degree of sequence identity between dystrophin and utrophin, it has been previously suggested that utrophin could in fact functionally compensate for the lack of dystrophin. Recent studies using transgenic mouse model systems have directly tested this hypothesis and revealed that upregulation of utrophin throughout dystrophic muscle fibres represents indeed, a viable approach for the treatment of DMD. Current studies are therefore focusing on the elucidation of the various regulatory mechanisms presiding over expression of utrophin in muscle fibres in attempts to ultimately identify small molecules which could systematically increase utrophin levels in extrasynaptic compartments of dystrophic muscle fibres. This review presents some of the recent data relevant for our understanding of the transcriptional regulatory mechanisms involved in maintaining expression of utrophin at the neuromuscular junction. In addition, the contribution of specific cues originating from motoneurons and the putative involvement of signalling events are also discussed.

Nerve-derived trophic factors and DNA elements controlling expression of genes encoding synaptic proteins in skeletal muscle fibers.

The neuromuscular junction represents an excellent model system for studying various critical issues in neurobiology at the molecular, cellular, and physiological levels. Our understanding of the basic events underlying synpase formation, maintenance, and plasticity has progressed considerably over the last few years primarily because of the numerous studies that have focused on this synapse and used sophisticated recombinant DNA technology. Recent data indicate that myonuclei located in the vicinity of the postsynaptic membrane are in a differential state of transcription compared to nuclei of the extrasynaptic sarcoplasm. Thus, renewal of postsynaptic membrane proteins appears to occur via a mechanism involving the local transcriptional activation of genes encoding these specialized proteins and extracellular cues originating from motoneurons. Such interaction between presynaptic nerve terminals and the postsynaptic sarcoplasm indicates that the entire signal transduction pathway is compartmentalized at the level of the neuromuscular junction. Expression of these genes appears less coregulated than originally anticipated, indicating that maintenance of the postsynaptic membrane requires the contribution of multiple extracellular signals, which ultimately urge target transcription factors to distinct DNA regulatory elements via various second messenger systems.

Muscle and neural isoforms of agrin increase utrophin expression in cultured myotubes via a transcriptional regulatory mechanism.

Duchenne muscular dystrophy is a prevalent X-linked neuromuscular disease for which there is currently no cure. Recently, it was demonstrated in a transgenic mouse model that utrophin could functionally compensate for the lack of dystrophin and alleviate the muscle pathology (Tinsley, J. M., Potter, A. C., Phelps, S. R., Fisher, R., Trickett, J. I., and Davies, K. E. (1996) Nature 384, 349-353). In this context, it thus becomes essential to determine the cellular and molecular mechanisms presiding over utrophin expression in attempts to overexpress the endogenous gene product throughout skeletal muscle fibers. In a recent study, we showed that the nerve exerts a profound influence on utrophin gene expression and postulated that nerve-derived trophic factors mediate the local transcriptional activation of the utrophin gene within nuclei located in the postsynaptic sarcoplasm (Gramolini, A. O., Dennis, C. L., Tinsley, J. M., Robertson, G. S., Davies, K. E, Cartaud, J., and Jasmin, B. J. (1997) J. Biol. Chem. 272, 8117-8120). In the present study, we have therefore focused on the effect of agrin on utrophin expression in cultured C2 myotubes. In response to Torpedo-, muscle-, or nerve-derived agrin, we observed a significant 2-fold increase in utrophin mRNAs. By contrast, CGRP treatment failed to affect expression of utrophin transcripts. Western blotting experiments also revealed that the increase in utrophin mRNAs was accompanied by an increase in the levels of utrophin. To determine whether these changes were caused by parallel increases in the transcriptional activity of the utrophin gene, we transfected muscle cells with a 1. 3-kilobase pair utrophin promoter-reporter (nlsLacZ) gene construct and treated them with agrin for 24-48 h. Under these conditions, both muscle- and nerve-derived agrin increased the activity of beta-galactosidase, indicating that agrin treatment led, directly or indirectly, to the transcriptional activation of the utrophin gene. Furthermore, this increase in transcriptional activity in response to agrin resulted from a greater number of myonuclei expressing the 1.3-kilobase pair utrophin promoter-nlsLacZ construct. Deletion of 800 base pairs 5' from this fragment decreased the basal levels of nlsLacZ expression and abolished the sensitivity of the utrophin promoter to exogenously applied agrin. In addition, site-directed mutagenesis of an N-box motif contained within this 800-base pair fragment demonstrated its essential contribution in this regulatory mechanism. Finally, direct gene transfer studies performed in vivo further revealed the importance of this DNA element for the synapse-specific expression of the utrophin gene along multinucleated muscle fibers. These data show that both muscle and neural isoforms of agrin can regulate expression of the utrophin gene and further indicate that agrin is not only involved in the mechanisms leading to the formation of clusters containing presynthesized synaptic molecules but that it can also participate in the local regulation of genes encoding synaptic proteins. Together, these observations are therefore relevant for our basic understanding of the events involved in the assembly and maintenance of the postsynaptic membrane domain of the neuromuscular junction and for the potential use of utrophin as a therapeutic strategy to counteract the effects of Duchenne muscular dystrophy.

Duchenne muscular dystrophy and the neuromuscular junction: the utrophin link.

Although the precise function of utrophin at the postsynaptic membrane of the neuromuscular junction still remains unclear, despite recent genetic 'knockout' experiments, a separate study in a transgenic mouse model system for Duchenne muscular dystrophy (DMD) has nonetheless shown that overexpression of utrophin into extrasynaptic regions of muscle fibers can functionally compensate for the lack of dystrophin and alleviate the muscle pathology. In this context, the next step is to identify the mechanisms presiding over expression of utrophin at the neuromuscular synapse in attempts to induce its expression throughout DMD muscle fibers. In fact, additional studies have shown that an important DNA element contained with the utrophin promoter may confer synapse-specific expression to the utrophin gene. Identification of the events culminating in the transactivation of the utrophin gene within synaptic myonuclei should provide important cues for the development of an effective therapeutic strategy for DMD.

Local transcriptional control of utrophin expression at the neuromuscular synapse.

Recently, the use of a transgenic mouse model system for Duchenne muscular dystrophy has demonstrated the ability of utrophin to functionally replace dystrophin and alleviate the muscle pathology (see Tinsley, J. M., Potter, A. C., Phelps, S. R., Fisher, R., Trickett, J. I., and Davies, K. E. (1996) Nature 384, 349-353). However, there is currently a clear lack of information concerning the regulatory mechanisms presiding over utrophin expression during normal myogenesis and synaptogenesis. Using in situ hybridization, we show that utrophin mRNAs selectively accumulate within the postsynaptic sarcoplasm of adult muscle fibers. In addition, we demonstrate that a 1.3-kilobase fragment of the human utrophin promoter is sufficient to confer synapse-specific expression to a reporter gene. Deletion of 800 base pairs from this promoter fragment reduces the overall expression of the reporter gene and abolishes its synapse-specific expression. Finally, we also show that utrophin is present at the postsynaptic membrane of ectopic synapses induced to form at sites distant from the original neuromuscular junctions. Taken together, these results indicate that nerve-derived factors regulate locally the transcriptional activation of the utrophin gene in skeletal muscle fibers and that myonuclei located in extrasynaptic regions are capable of expressing utrophin upon receiving appropriate neuronal cues.