Ulrike Zeiger

Quantitative Proteomics Profiling of Sarcomere Associated Proteins in Limb and Extraocular Muscle Allotypes

The sarcomere is the major structural and functional unit of striated muscle. Approximately 65 different proteins have been associated with the sarcomere, and their exact composition defines the speed, endurance, and biology of each individual muscle. Past analyses relied heavily on electrophoretic and immunohistochemical techniques, which only allow the analysis of a small fraction of proteins at a time. Here we introduce a quantitative label-free, shotgun proteomics approach to differentially quantitate sarcomeric proteins from microgram quantities of muscle tissue in a fast and reliable manner by liquid chromatography and mass spectrometry. The high sequence similarity of some sarcomeric proteins poses a problem for shotgun proteomics because of limitations in subsequent database search algorithms in the exclusive assignment of peptides to specific isoforms. Therefore multiple sequence alignments were generated to improve the identification of isoform specific peptides. This methodology was used to compare the sarcomeric proteome of the extraocular muscle allotype to limb muscle. Extraocular muscles are a unique group of highly specialized muscles with distinct biochemical, physiological, and pathological properties. We were able to quantitate 40 sarcomeric proteins; although the basic sarcomeric proteins in extraocular muscle are similar to those in limb muscle, key proteins stabilizing the connection of the Z-bands to thin filaments and the costamere are augmented in extraocular muscle and may represent an adaptation to the eccentric contractions known to normally occur during eye movements. Furthermore, a number of changes are seen that closely relate to the unique nature of extraocular muscle.

Comparison of the myoplasmic calcium transient elicited by an action potential in intact fibres of mdx and normal mice

The myoplasmic free [Ca2+] transient elicited by an action potential (Δ[Ca2+]) was compared in fast‐twitch fibres of mdx (dystrophin null) and normal mice. Methods were used that maximized the likelihood that any detected differences apply in vivo. Small bundles of fibres were manually dissected from extensor digitorum longus muscles of 7‐ to 14‐week‐old mice. One fibre within a bundle was microinjected with furaptra, a low‐affinity rapidly responding fluorescent calcium indicator. A fibre was accepted for study if it gave a stable, all‐or‐nothing fluorescence response to an external shock. In 18 normal fibres, the peak amplitude and the full‐duration at half‐maximum (FDHM) of Δ[Ca2+] were 18.4 ± 0.5 μm and 4.9 ± 0.2 ms, respectively (mean ±s.e.m.; 16°C). In 13 mdx fibres, the corresponding values were 14.5 ± 0.6 μm and 4.7 ± 0.2 ms. The difference in amplitude is statistically highly significant (P= 0.0001; two‐tailed t test), whereas the difference in FDHM is not (P= 0.3). A multi‐compartment computer model was used to estimate the amplitude and time course of the sarcoplasmic reticulum (SR) calcium release flux underlying Δ[Ca2+]. Estimates were made based on several differing assumptions: (i) that the resting myoplasmic free Ca2+ concentration ([Ca2+]R) and the total concentration of parvalbumin ([ParvT]) are the same in mdx and normal fibres, (ii) that [Ca2+]R is larger in mdx fibres, (iii) that [ParvT] is smaller in mdx fibres, and (iv) that [Ca2+]R is larger and [ParvT] is smaller in mdx fibres. According to the simulations, the 21% smaller amplitude of Δ[Ca2+] in mdx fibres in combination with the unchanged FDHM of Δ[Ca2+] is consistent with mdx fibres having a ∼25% smaller flux amplitude, a 6–23% larger FDHM of the flux, and a 9–20% smaller total amount of released Ca2+ than normal fibres. The changes in flux are probably due to a change in the gating of the SR Ca2+‐release channels and/or in their single channel flux. The link between these changes and the absence of dystrophin remains to be elucidated.

Superior calcium homeostasis of extraocular muscles.

Extraocular muscles (EOMs) are a unique group of skeletal muscles with unusual physiological properties such as being able to undergo rapid twitch contractions over extended periods and escape damage in the presence of excess intracellular calcium (Ca(2+)) in Duchennes muscular dystrophy (DMD). Enhanced Ca(2+) buffering has been proposed as a contributory mechanism to explain these properties; however, the mechanisms are not well understood. We investigated mechanisms modulating Ca(2+) levels in EOM and tibialis anterior (TA) limb muscles. Using Fura-2 based ratiometric Ca(2+) imaging of primary myotubes we found that EOM myotubes reduced elevated Ca(2+) ˜2-fold faster than TA myotubes, demonstrating more efficient Ca(2+) buffering. Quantitative PCR (qPCR) and western blotting revealed higher expression of key components of the Ca(2+) regulation system in EOM, such as the cardiac/slow isoforms sarcoplasmic Ca(2+)-ATPase 2 (Serca2) and calsequestrin 2 (Casq2). Interestingly EOM expressed monomeric rather than multimeric forms of phospholamban (Pln), which was phosphorylated at threonine 17 (Thr17) but not at the serine 16 (Ser16) residue. EOM Pln remained monomeric and unphosphorylated at Ser16 despite protein kinase A (PKA) treatment, suggesting differential signalling and modulation cascades involving Pln-mediated Ca(2+) regulation in EOM. Increased expression of Ca(2+)/SR mRNA, proteins, differential post-translational modification of Pln and superior Ca(2+) buffering is consistent with the improved ability of EOM to handle elevated intracellular Ca(2+) levels. These characteristics provide mechanistic insight for the potential role of superior Ca(2+) buffering in the unusual physiology of EOM and their sparing in DMD.

Identification of the Neuromuscular Junction Transcriptome of Extraocular Muscle by Laser Capture Microdissection

PURPOSE To examine and characterize the profile of genes expressed at the synapses or neuromuscular junctions (NMJs) of extraocular muscles (EOMs) compared with those expressed at the tibialis anterior (TA). METHODS Adult rat eyeballs with rectus EOMs attached and TAs were dissected, snap frozen, serially sectioned, and stained for acetylcholinesterase (AChE) to identify the NMJs. Approximately 6000 NMJs for rectus EOM (EOMsyn), 6000 NMJs for TA (TAsyn), equal amounts of NMJ-free fiber regions (EOMfib, TAfib), and underlying myonuclei and RNAs were captured by laser capture microdissection (LCM). RNA was processed for microarray-based expression profiling. Expression profiles and interaction lists were generated for genes differentially expressed at synaptic and nonsynaptic regions of EOM (EOMsyn versus EOMfib) and TA (TAsyn versus TAfib). Profiles were validated by using real-time quantitative polymerase chain reaction (qPCR). RESULTS The regional transcriptomes associated with NMJs of EOMs and TAs were identified. Two hundred seventy-five genes were preferentially expressed in EOMsyn (compared with EOMfib), 230 in TAsyn (compared with TAfib), and 288 additional transcripts expressed in both synapses. Identified genes included novel genes as well as well-known, evolutionarily conserved synaptic markers (e.g., nicotinic acetylcholine receptor (AChR) alpha (Chrna) and epsilon (Chrne) subunits and nestin (Nes). CONCLUSIONS Transcriptome level differences exist between EOM synaptic regions and TA synaptic regions. The definition of the synaptic transcriptome provides insight into the mechanism of formation and functioning of the unique synapses of EOM and their differential involvement in diseases noted in the EOM allotype.

Expression Profiling Reveals Novel Hypoxic Biomarkers in Peripheral Blood of Adult Mice Exposed to Chronic Hypoxia

Hypoxia induces a myriad of changes including an increase in hematocrit due to erythropoietin (EPO) mediated erythropoiesis. While hypoxia is of importance physiologically and clinically, lacunae exist in our knowledge of the systemic and temporal changes in gene expression occurring in blood during the exposure and recovery from hypoxia. To identify these changes expression profiling was conducted on blood obtained from cohorts of C57Bl-10 wild type mice that were maintained at normoxia (NX), exposed for two weeks to normobaric chronic hypoxia (CH) or two weeks of CH followed by two weeks of normoxic recovery (REC). Using stringent bioinformatic cut-offs (0% FDR, 2 fold change cut-off), 230 genes were identified and separated into four distinct temporal categories. Class I) contained 1 transcript up-regulated in both CH and REC; Class II) contained 202 transcripts up-regulated in CH but down-regulated after REC; Class III) contained 9 transcripts down-regulated both in CH and REC; Class IV) contained 18 transcripts down-regulated after CH exposure but up-regulated after REC. Profiling was independently validated and extended by analyzing expression levels of selected genes as novel biomarkers from our profile (e.g. spectrin alpha-1, ubiquitin domain family-1 and pyrroline-5-carboxylate reductase-1) by performing qPCR at 7 different time points during CH and REC. Our identification and characterization of these genes define transcriptome level changes occurring during chronic hypoxia and normoxic recovery as well as novel blood biomarkers that may be useful in monitoring a variety of physiological and pathological conditions associated with hypoxia.