Clinical integration of next-generation sequencing technology.

Recent advances in next-generation sequencing (NGS) methods and technology have substantially reduced costs and operational complexity leading to production of benchtop sequencers and commercial software solutions for implementation in small research and clinical laboratories. This article addresses requirements and limitations to successful implementation of these systems, including (1) calibration and validation of the instrumentation, experimental paradigm, and primary readout, (2) secure data transfer, storage, and secondary processing, (3) implementation of software tools for targeted analysis, and (4) training of research and clinical personnel to evaluate data fidelity and interpret the molecular significance of the genomic output.

Proteins secreted by embryonic stem cells activate cardiomyocytes through ligand binding pathways.

Human embryonic stem cells (hESC) underlie embryogenesis but paracrine signals associated with the process are unknown. This study was designed to 1) profile native proteins secreted by undifferentiated hESC and 2) determine their biological effects on primary neonatal cardiomyocytes. We utilized multi-analyte, immunochemical assays to characterize media conditioned by undifferentiated hESC versus unconditioned media. Expression profiling was performed on cardiomyocytes subjected to these different media conditions and altered transcripts were mapped to critical pathways. Thirty-two of 109 proteins were significantly elevated in conditioned media ranging in concentration from thrombospondin (57.2+/-5.0 ng/ml) to nerve growth factor (7.4+/-1.2pg/ml) and comprising chemokines, cytokines, growth factors, and proteins involved in cell adhesion and extracellular matrix remodeling. Conditioned media induced karyokinesis, cytokinesis and proliferation in mono- and binucleate cardiomyocytes. Pathway analysis revealed comprehensive activation of the ROCK 1 and 2 G-protein coupled receptor (GPCR) pathway associated with cytokinesis, and the RAS/RAF/MEK/ERK receptor tyrosine kinase (RTK) and JAK/STAT-cytokine pathway involved in cell cycle progression. These results provide a partial database of proteins secreted by pluripotent hESC that potentiate cell division in cardiomyocytes via a paracrine mechanism suggesting a potential role for these stem cell factors in cardiogenesis and cardiac repair.

Acute molecular response of mouse hindlimb muscles to chronic stimulation.

Stimulation of the mouse hindlimb via the sciatic nerve was performed for a 4-h period to investigate acute muscle gene activation in a model of muscle phenotype conversion. Initial force production (1.6 +/- 0.1 g/g body wt) declined 45% within 10 min and was maintained for the remainder of the experiment. Force returned to initial levels upon study completion. An immediate-early growth response was present in the extensor digitorum longus (EDL) muscle (FOS, JUN, activating transcription factor 3, and musculoaponeurotic fibrosarcoma oncogene) with a similar but attenuated pattern in the soleus muscle. Transcript profiles showed decreased fast fiber-specific mRNA (myosin heavy chains 2A and 2B, fast troponins T(3) and I, alpha-tropomyosin, muscle creatine kinase, and parvalbumin) and increased slow transcripts (myosin heavy chain-1beta/slow, troponin C slow, and tropomyosin 3y) in the EDL versus soleus muscles. Histological analysis of the EDL revealed glycogen depletion without inflammatory cell infiltration in stimulated versus control muscles, whereas ultrastructural analysis showed no evidence of myofiber damage after stimulation. Multiple fiber type-specific transcription factors (tea domain family member 1, nuclear factor of activated T cells 1, peroxisome proliferator-activated receptor-gamma coactivator-1alpha and -beta, circadian locomotor output cycles kaput, and hypoxia-inducible factor-1alpha) increased in the EDL along with transcription factors characteristic of embryogenesis (Kruppel-like factor 4; SRY box containing 17; transcription factor 15; PBX/knotted 1 homeobox 1; and embryonic lethal, abnormal vision). No established in vivo satellite cell markers or genes activated in our parallel experiments of satellite cell proliferation in vitro (cyclins A(2), B(2), C, and E(1) and MyoD) were differentially increased in the stimulated muscles. These results indicated that the molecular onset of fast to slow phenotype conversion occurred in the EDL within 4 h of stimulation without injury or satellite cell recruitment. This conversion was associated with the expression of phenotype-specific transcription factors from resident fiber myonuclei, including the activation of nascent developmental transcriptional programs.

Gene expression changes in peripheral blood mononuclear cells from multiple sclerosis patients undergoing beta-interferon therapy.

OBJECTIVE: Multiple sclerosis (MS) is a disabling idiopathic inflammatory disorder with evidence of immune dysfunction. Current therapies for MS include preparations of beta-interferon (beta IFN). We studied the gene expression patterns in peripheral blood mononuclear cells from relapsing-remitting MS patients undergoing weekly beta IFN-1a therapy (Avonex; 30 mg intramuscular) to identify biomarkers for beta IFN responsiveness. METHODS: Oligonucleotide microarrays were used for the comparative analysis of gene expression patterns from longitudinal PBMC samples taken from five patients undergoing beta IFN therapy. RESULTS: On the basis of two-fold changes in expression levels and statistical analyses we selected a candidate diagnostic set of 136 genes that were differentially expressed between pretreatment and IFN-beta-1a-treated MS patients. When we applied this gene set to cluster the specimens according to their expression profiles, the pretreatment samples clustered in one branch, and acute and chronic samples following treatment clustered in another branch. However, the chronic samples from the single clinical non-responder clustered with the pretreatment branch, suggesting that a possible reversal of beta IFN-induced gene expression may be contributing to the poor clinical response. CONCLUSIONS: These 136 genes represent potential targets for new MS therapeutics and the basis for lack of beta IFN response.

Cardiac fibroblasts influence cardiomyocyte phenotype in vitro.

Cardiac fibroblasts impact myocardial development and remodeling through intercellular contact with cardiomyocytes, but less is known about noncontact, profibrotic signals whereby fibroblasts alter cardiomyocyte behavior. Fibroblasts and cardiomyocytes were harvested from newborn rat ventricles and separated by serial digestion and gradient centrifugation. Cardiomyocytes were cultured in 1) standard medium, 2) standard medium diluted 1:1 with PBS, or 3) standard medium diluted 1:1 with medium conditioned > or =72 h by cardiac fibroblasts. Serum concentrations were held constant under all media conditions, and complete medium exchanges were performed daily. Cardiomyocytes began contracting within 24 h at clonal or mass densities with <5% of cells expressing vimentin. Immunocytochemical analysis revealed progressive expression of alpha-smooth muscle actin in cardiomyocytes after 24 h in all conditions. Only cardiomyocytes in fibroblast-conditioned medium stopped contracting by 72 h. There was a significant, sustained increase in vimentin expression specific to these cultures (means +/- SD: conditioned 46.3 +/- 6.0 vs. control 5.3 +/- 2.9%, P < 0.00025) typically with cardiac myosin heavy chain coexpression. Proteomics assays revealed 10 cytokines (VEGF, GRO/KC, monocyte chemoattractant protein-1, leptin, macrophage inflammatory protein-1alpha, IL-6, IL-10, IL-12p70, IL-17, and tumor necrosis factor-alpha) at or below detection levels in unconditioned medium that were significantly elevated in fibroblast-conditioned medium. Latent transforming growth factor-beta and RANTES were present in unconditioned medium but rose to higher levels in conditioned medium. Only granulocyte-macrophage colony-stimulating factor was present above threshold levels in standard medium but decreased with fibroblast conditioning. These data indicated that under the influence of fibroblast-conditioned medium, cardiomyocytes exhibited marked hypertrophy, diminished contractile capacity, and phenotype plasticity distinct from the dedifferentiation program present under standard culture conditions.

Molecular dynamics of the compensatory response to myocardial infarct.

Myocardial infarct via occlusion of the left anterior descending coronary in rats caused overriding depression in transcription, signal transduction, inflammation and extracellular matrix pathways in the infarct zone within 24 h. In contrast, remote zone gene expression was reciprocally activated during the immediate post-infarct period. Infarct zone signal transduction occurred primarily through TGFbeta1 induction while the remote zone exhibited elevated WNT, NOTCH, GPCR and transmembrane signaling. A minimal day 1 acute phase, inflammatory response was detected in the infarct zone while interleukins (IL1alpha, IL1beta, IL6, IL12alpha, IL18) and the TNFalpha superfamily were activated in the remote zone. Different cytochrome subsets were activated in each left ventricular region on day 1 while anti-oxidant genes were elevated only in the remote zone. The infarct zone exhibited mixed early transcription factor activation across all binding domains with a balance favoring constitutive gene activation and differentiation pathways as opposed to cell proliferation. In contrast, the remote zone exhibited activation of extensive developmental transcription factors involved in specification of cell phenotype, tissue-specific interactions and position-specific cell proliferation on day 1. The day 28 infarct zone response mirrored the day 1 remote zone response including activation of genes associated with matrix remodeling (metallothionein and metalloproteinase 9, 12, 23), as well as genes associated with cell proliferation and phenotype specification (MYC, EGR2, ATF3, HOXA1) recapitulating developmental histogenesis programs.

Effect of muscle origin and phenotype on satellite cell muscle-specific gene expression.

Satellite cells from adult mouse tongue, diaphragm, vastus lateralis, rectus femoris, tibialis anterior, soleus, and extensor digitorum longus muscles were isolated, expanded, and differentiated under identical culture conditions. Proliferating myoblasts and differentiated myofiber cultures were analyzed via SDS-PAGE, immunochemical, and PCR methods for expression of myosin heavy chains (MyHC) and muscle creatine kinase (MCK) as indices of muscle fiber type. Contralateral muscles were harvested for simultaneous, parallel analysis utilizing these assays. The MyHC profile of differentiated primary satellite cells was equivalent across all cultures with MyHC(2A) and MyHC(1/slow) co-expressed in all myotube and myofiber structures. Trace amounts of MyHC(2B) and MyHC(neo) were detected in a few myofibers. MCK was expressed at a uniform, similar level among these cultures. In contrast, contralateral muscles expressed each muscle-specific indicator at levels correlated with the fiber-type distribution within each muscle. MM14 and C2C12 cells, mouse satellite cell lines, were expanded and compared to primary cell cultures. MM14 cells had a high differentiation index (>95%) and co-expressed MyHC(2A) and MyHC(1/slow) along with trace amounts of MyHC(neo) throughout myotube cultures. Myofibers obtained from C2C12 cells exhibited less differentiation (~75%) with MyHC(2A) as the dominant isoform. These data indicate that primary satellite cells from adult muscle form a uniform differentiated cell type regardless of the fiber-type, anatomic location, and embryonic origin of the donor muscles. MM14 cells expressed an adult MyHC isoform profile similar to primary satellite cells. The results suggest that satellite cells provide a uniform cell source for use in autologous transplantation studies and do not acquire a heritable fiber-type-specific phenotype from their host muscle.

Cutaneous wound analysis using hyperspectral imaging.

A correlative bright-field and hyperspectral analysis of full-thickness, cutaneous wounds in a porcine model was undertaken to investigate the efficacy of hyperspectral imaging as an alternate method for wound identification. Analysis of a randomly selected specimen yielded distinct spectral signatures for cutaneous regions of interest including the epidermis, injured dermis, and normal dermis. The scanning of the entire specimen group using these hyperspectral signatures revealed an exclusionary, pseudo-color pattern whereby a central wound region was consistently defined by a unique spectral signature. An algorithm was derived as an objective tool for the comparison of the wound regions defined by the hyperspectral classification versus the pathologists' manual tracings. The dimensions of the wound identified in the hyperspectral assay did not differ significantly from the wound region identified by the pathologists using standard bright-field microscopy. These data indicate that hyperspectral analysis may provide a high-throughput alternative for wound estimation that approximates standard bright-field imaging and pathologist evaluation.

Muscle type-specific myosin isoforms in crustacean muscles.

Differential expression of multiple myosin heavy chain (MyHC) genes largely determines the diversity of critical physiological, histochemical, and enzymatic properties characteristic of skeletal muscle. Hypotheses to explain myofiber diversity range from intrinsic control of expression based on myoblast lineage to extrinsic control by innervation, hormones, and usage. The unique innervation and specialized function of crayfish (Procambarus clarkii) appendicular and abdominal musculature provide a model to test these hypotheses. The leg opener and superficial abdominal extensor muscles are innervated by tonic excitatory motoneurons. High resolution SDS-PAGE revealed that these two muscles express the same MyHC profile. In contrast, the deep abdominal extensor muscles, innervated by phasic motoneurons, express MyHC profiles different from the tonic profiles. The claw closer muscles are dually innervated by tonic and phasic motoneurons and a mixed phenotype was observed, albeit biased toward the phasic profile seen in the closer muscle. These results indicate that multiple MyHC isoforms are present in the crayfish and that differential expression is associated with diversity of muscle type and function.

Muscle tissue engineering.

Only recently have scientists come to appreciate that many tissues and cell populations that were formerly considered to be in a terminally differentiated state are capable of division and or dedifferentiation. It is the goal of the tissue engineer to understand and redirect this potential. Muscle tissue-engineering efforts will be directed toward building in vitro replacements for in vivo problems. Tissue-engineering advances will be interdependent with advances in gene therapy techniques to restore function at a cellular level.

Functional properties of conditioned skeletal muscle: implications for muscle-powered cardiac assist.

Latissimus dorsi (LD) muscles of six canines were studied to assess changes induced by electrical conditioning and to quantify the capacity of these muscles to perform hemodynamic work. Muscles were conditioned using burst stimuli delivered over an 8-wk period. Contralateral LD were used as control. Muscles were tested in situ to simulate anticipated linear-pull cardiac assist conditions. This training process reduced muscle mass and cross-sectional area by 16 and 17%, respectively. Muscle phenotype shifted to a predominantly "slow" form by coordinate reduction of myosin heavy chain (MHC) 2A expression and increased expression of the MHC beta/slow form. Force generation was reduced by 54%, and contractile duration increased 13%. Fatigue resistance was markedly enhanced, and chronic stroke work increased from 0.19 to 0.72 mJ/g. The highest steady-state power output (2.06 mW/g) was obtained from one muscle fully converted to a slow phenotype. These data suggest that single LD trained via conventional techniques can provide energy sufficient for partial cardiac assistance but cannot sustain work levels needed to achieve total circulatory support.

Activity-dependent induction of slow myosin gene expression in isolated fast-twitch mouse muscle.

We demonstrate that direct electrical stimulation of isolated fast-twitch muscle in an organ culture system can induce expression of the slow myosin heavy chain (beta-MHC) gene, indicative of a phenotype transformation. Pairs of extensor digitorum longus (EDL) muscles were isolated from adult mice, incubated at resting length in separate chambers, and superfused with the same recirculated media One muscle was subjected to twitch stimulation (5-s trains of 5-Hz pulses at supramaximal voltage every minute), and force was recorded to assess function. The contralateral muscle was incubated without stimulation, to control for effects of the experimental preparation. Both muscle were rapidly frozen for RNA purification and oligo(dT)-primed reverse transcription; serial studies were carried out to 36 h. Polymerase chain reaction was performed utilizing primers specific for cytoplasmic beta-actin (beta-actin), a constitutive marker, and beta-MHC, a gene that is either inactive or expressed at very low levels in control EDL. After 30 h of stimulation, beta-MHC was consistently detected at a level severalfold higher in stimulated EDL than in incubated control EDL when band intensities were normalized to those of beta-actin. These results show that signals or fiber-specific transformations reside within the muscle and that this shift begins rapidly after induction of continuous stimulation.

Harvest protocol to reduce variability of soluble enzyme yield from cultured cells.

Many aspects of physiology and gene regulation can be studied by examining the levels of enzymes harvested from cultured cells. We found that the yield from cultured cells of two different cytosolic enzymes, creatine kinase and the common reporter gene product chloramphenicol acetyltransferase (CAT), could be highly variable despite superficially identical harvest procedures. Analysis of multiple harvest and assay parameters disclosed that fluctuations in enzyme yield were correlated with the time cells that were allowed to remain in an EDTA-containing buffered saline solution prior to scraping from the dishes with a rubber policeman. The highest and most consistent yields were obtained when the cells were allowed to remain in the solution for 6-10 min before scraping: this protocol has cut variability approximately by a factor of three.

Postnatal expression of myosin isoforms in the genioglossus and diaphragm muscles.

We studied the expression of myosin heavy chain (MHC) and native myosin isoforms in the genioglossus (GG) and costal diaphragm (DIA) muscles of the rat during postnatal development using both denaturing and nondenaturing gel electrophoresis. Primary myotubes in both fast and slow muscles homogeneously express slow as well as embryonic myosin. Since the adult GG is comprised primarily of fast MHC isoforms, whereas the adult DIA is characterized by a mixture of MHC slow and fast isoforms, we hypothesized that the GG and DIA would be subject to different temporal patterns of MHC isoform expression during postnatal development. Native myosin and MHC gels demonstrated a persistence of neonatal MHC (MHC neo) on day 25 in the GG, whereas this isoform was not detected beyond day 21 in the DIA. The MHC phenotype in GG of the adult demonstrated a predominance of MHC 2X (35% +/- 8) and MHC 2B (45% +/- 10) with a smaller proportion of MHC 2A (19% +/- 5). In contrast, the MHC phenotype in adult DIA was characterized by approximately equal proportions of MHC slow (25% +/- 3), MHC 2A (34% +/- 10), and MHC 2X (31% +/- 12) with a small percentage of MHC 2B (9% +/- 7). These data suggest that postnatal regulation of MHC expression in the GG and DIA is muscle specific.

Postnatal expression of myosin isoforms in an expiratory muscle--external abdominal oblique.

We studied the postnatal expression of heavy-chain (MHC) and native myosin isoforms in an expiratory abdominal muscle of the rat, the external abdominal oblique (EO). Moreover, we contrasted EO myosin expression with that of the costal diaphragm (DIA) to draw inspiratory vs. expiratory muscle comparisons during development. Examination of MHC gels demonstrated a mature phenotype of slow and adult fast myosin isoforms at an earlier age in the EO (day 60) than in the DIA [day > 115 (adult)]. The mature MHC phenotype of the EO was characterized by a preponderance of MHC 2B, whereas the DIA was characterized by approximately equal portions of MHC slow, MHC 2A, and MHC 2X. During early postnatal development, there was a delay in the expression of MHC 2A in the EO compared with the DIA. However, MHC 2B, expressed later in development in both muscles, was noted in the EO before the DIA. We conclude that 1) the EO mature myosin phenotype is characterized by a preponderance of fast myosin isoforms and 2) the EO and DIA muscles are subject to different temporal patterns of isoform expression during postnatal development.

Myosin heavy chain expression in respiratory muscles of the rat.

Myosin heavy chain (MHC) isoforms of hind limb adult rat muscles and muscles with a range of respiratory activities were analyzed by a sodium dodecyl sulfate polyacrylamide gel electrophoresis technique that allowed electrophoretic separation of the three fast and one slow MHC isoform found in typical rat muscle. Costal and crural diaphragm muscle samples expressed a mixture of MHC beta/slow, MHC2A, and MHC2X but little MHC2B. In contrast, MHC2B was the dominant MHC isoform in the genioglossus, intercostal, and three abdominal muscles, all of which exhibited minimal expression of MHC beta/slow. The amount of MHC2X (relative to total MHC composition) was similar in the diaphragm, genioglossus, and transversus abdominis muscles, while considerably less was detected in the rectus abdominis and external oblique muscles. These results indicate that MHC2X is broadly and variably distributed among respiratory muscles. Furthermore, these data suggest that a large portion of 2X fibers (containing MHC2X), which cannot be detected by standard histochemical analysis, may be present in the genioglossus and transversus abdominis muscles as has been demonstrated for the diaphragm muscle. We speculate that an association exists between the level of MHC2X expression and frequency of respiratory recruitment.

Effects of perinatal undernutrition on elimination of immature myosin isoforms in the rat diaphragm.

The effect of perinatal undernutrition on the postnatal elimination of immature myosin isoforms in rat diaphragm muscle was examined using electrophoretic and immunocytochemical techniques. Electrophoresis of native myosin showed that neonatal bands were present in diaphragm muscles of both control and undernourished rats on day 4. By day 21, the neonatal bands were diminished in the control diaphragm compared with the diaphragm of the undernourished rats. Neonatal bands persisted on postnatal day 30 in the diaphragm of the undernourished rats but not in the diaphragm of control rats. No significant difference in the time course of elimination of embryonic myosin light chain (LCemb) was observed between the diaphragm muscles of control and undernourished rats with two-dimensional gel electrophoresis. Immunocytochemical analysis demonstrated embryonic myosin heavy chain (MHCemb) in all myofibers of the diaphragm muscle of both groups at day 4, but this isoform was not detected in either group by day 14. Reactivity with anti-neonatal myosin heavy chain (MHCneo) indicated that rate of elimination of the MHCneo was delayed in the undernourished state as compared with the normal rats (P less than 0.001). Serum triiodothyronine levels were measured at 14, 21, and 30 days and were significantly lower in the undernourished rats compared with age-matched controls. These data demonstrate that the normal postnatal decrease in MHCneo, but not MHCemb or LCemb, is affected by the nutritional state of the animal. We speculate that these alterations in myosin isoform transitions are induced by hypothyroidism associated with undernutrition.

Uniform myosin isoforms in the flight muscles for little brown bats, Myotis lucifugus.

The present study used muscle histochemistry and polyacrylamide gel electrophoresis of native myosin and myosin heavy chains to establish a correlation, if any, between chiropteran histochemical fiber types and myosin isoform composition. Histochemical analysis of the primary flight muscle, the pectoralis profundus, documented the presence of a single histochemical fiber type, here termed Type II. Electrophoresis of native myosin isolated from pectoralis muscle yielded a single isoform that comigrated with the FM-3 isoform of rat diaphragm. Heavy chain analysis of the Myotis pectoralis demonstrated a single heavy chain with comparable electrophoretic mobility to rat IIa myosin heavy chain. These data demonstrate unique histochemical and biochemical homogeneity in the myosin composition of the pectoralis muscle of Myotis lucifugus. Thus this muscle is extremely specialized for flight at histochemical, morphologic, and molecular levels. These data contrast with the mixed myosin and histochemical fiber types found in other mammals, as well as in other muscles of Myotis lucifugus.

Emergence of the mature myosin phenotype in the rat diaphragm muscle.

Immunohistochemical analysis of myosin heavy chain (MHC) isoform expression in perinatal and adult rat diaphragm muscles was performed with antibodies which permitted the identification of all known MHC isoforms found in typical rat muscles. Isoform switching, leading to the emergence of the adult phenotype, was more complex than had been previously described. As many as four isoforms could be coexpressed in a single myofiber. Elimination of developmental isoforms did not usually result in the myofiber immediately achieving its adult phenotype. Activation of genes for specific adult isoforms might be delayed to puberty. For example, two of the three fast MHCs, MHC2X and MHC2A appeared perinatally, while MHC2B did not appear until 30 days postnatal. By Day 60 this isoform was present in approximately 27% of the myofibers, but in most myofibers expression of this isoform was transient (i.e., at Day greater than or equal to 115, less than 4% of the myofibers expressed MHC2B). Fibers which contained MHC beta/slow during the late fetal and early neonatal period coexpressed MHCemb. A marked increase in the frequency of fibers containing MHC beta/slow occurred between 4 and 21 days postnatal. These slow fibers arose from a population of myofibers which expressed MHCemb and MHCneo during their development, and they accounted for the majority of slow fibers found in the adult diaphragm. The adult myosin phenotype of the diaphragm myofibers (as determined with immunocytochemistry, and 5% SDS-PAGE) was not achieved until the rat was greater than or equal to 115 days old.

Correlation of myosin isoforms with anatomical divisions in equine musculus biceps brachii.

The biceps brachii of horses is subdivided into a lateral and medial head. Electrophoresis of samples from the lateral head revealed three slow-migrating native myosin isoforms, including one that does not correspond to slow myosin isoforms described for other mammalian muscles. In contrast, the medial head contained a single slow isoform. Both the lateral and medial heads contained three fast-migrating isoforms corresponding with the FM-2, FM-3 and FM-4 isoforms reported for other mammalian fast-twitch muscle fibers. Electrophoresis of myosin heavy chains (MHCs) revealed only two MHC bands, one fast-migrating band that comigrates with rat type I MHC and a second slower-migrating band that comigrates with rat type IIa MHC. Quantitation of the histochemical data is correlated with densitometric analysis of MHCs in the medial and lateral heads of biceps brachii and is consistent with previously hypothesized functional specializations of this muscle.