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1.  Asynchronous remodeling is a driver of failed regeneration in Duchenne muscular dystrophy 
The Journal of Cell Biology  2014;207(1):139-158.
In Duchenne muscular dystrophy, asynchronous regeneration in microenvironments within muscle tissue results in development of fibrosis in lieu of global muscle recovery.
We sought to determine the mechanisms underlying failure of muscle regeneration that is observed in dystrophic muscle through hypothesis generation using muscle profiling data (human dystrophy and murine regeneration). We found that transforming growth factor β–centered networks strongly associated with pathological fibrosis and failed regeneration were also induced during normal regeneration but at distinct time points. We hypothesized that asynchronously regenerating microenvironments are an underlying driver of fibrosis and failed regeneration. We validated this hypothesis using an experimental model of focal asynchronous bouts of muscle regeneration in wild-type (WT) mice. A chronic inflammatory state and reduced mitochondrial oxidative capacity are observed in bouts separated by 4 d, whereas a chronic profibrotic state was seen in bouts separated by 10 d. Treatment of asynchronously remodeling WT muscle with either prednisone or VBP15 mitigated the molecular phenotype. Our asynchronous regeneration model for pathological fibrosis and muscle wasting in the muscular dystrophies is likely generalizable to tissue failure in chronic inflammatory states in other regenerative tissues.
doi:10.1083/jcb.201402079
PMCID: PMC4195829  PMID: 25313409
2.  Mexiletine for Treatment of Myotonia 
JAMA  2012;308(13):1377-1378.
doi:10.1001/jama.2012.12906
PMCID: PMC4352340  PMID: 23032555
3.  Pharmacologic Management of Duchenne Muscular Dystrophy: Target Identification and Preclinical Trials 
ILAR Journal  2014;55(1):119-149.
Duchenne muscular dystrophy (DMD) is an X-linked human disorder in which absence of the protein dystrophin causes degeneration of skeletal and cardiac muscle. For the sake of treatment development, over and above definitive genetic and cell-based therapies, there is considerable interest in drugs that target downstream disease mechanisms. Drug candidates have typically been chosen based on the nature of pathologic lesions and presumed underlying mechanisms and then tested in animal models. Mammalian dystrophinopathies have been characterized in mice (mdx mouse) and dogs (golden retriever muscular dystrophy [GRMD]). Despite promising results in the mdx mouse, some therapies have not shown efficacy in DMD. Although the GRMD model offers a higher hurdle for translation, dogs have primarily been used to test genetic and cellular therapies where there is greater risk. Failed translation of animal studies to DMD raises questions about the propriety of methods and models used to identify drug targets and test efficacy of pharmacologic intervention. The mdx mouse and GRMD dog are genetically homologous to DMD but not necessarily analogous. Subcellular species differences are undoubtedly magnified at the whole-body level in clinical trials. This problem is compounded by disparate cultures in clinical trials and preclinical studies, pointing to a need for greater rigor and transparency in animal experiments. Molecular assays such as mRNA arrays and genome-wide association studies allow identification of genetic drug targets more closely tied to disease pathogenesis. Genes in which polymorphisms have been directly linked to DMD disease progression, as with osteopontin, are particularly attractive targets.
doi:10.1093/ilar/ilu011
PMCID: PMC4158345  PMID: 24936034
animal models; drug development; Duchenne muscular dystrophy; golden retriever muscular dystrophy; genome wide association studies; mRNA arrays; mdx mouse; preclinical studies
4.  Short Read (Next-gen) Sequencing: A Tutorial with Cardiomyopathy Diagnostics as an Exemplar 
doi:10.1161/CIRCGENETICS.113.000085
PMCID: PMC4116683  PMID: 23852418
next-gen sequencing; titin; dilated cardiomyopathy; exome; cardiomyopathy; genetics; human
5.  A Renaissance for Antisense Oligonucleotide Drugs in Neurology 
Archives of neurology  2009;66(1):32-38.
Antisense oligonucleotides are short nucleic acid sequences designed for use as small-molecule drugs. They recognize and bind to specific messenger RNA (mRNA) or pre-mRNA sequences to create small double-stranded regions of the target mRNA that alter mRNA splicing patterns or inhibit protein translation. Antisense approaches have been actively pursued as a form of molecular medicine for more than 20 years, but only one has been translated to a marketed drug (intraocular human immunodeficiency virus treatment). Two recent advances foreshadow a change in clinical applications of antisense strategies. First is the development of synthetic DNA analogues that show outstanding stability and sequence specificity yet little or no binding to modulator proteins. Second is the publication of impressive preclinical and clinical data using antisense in an exon-skipping strategy to increase dystrophin production in Duchenne muscular dystrophy. As long-standing barriers are successfully circumvented, attention turns toward scale-up of production, long-term toxicity studies, and the challenges to traditional drug regulatory attitudes presented by tightly targeted sequence-specific drugs.
doi:10.1001/archneurol.2008.540
PMCID: PMC4111150  PMID: 19139297
6.  Alterations in Osteopontin Modify Muscle Size in Females in Both Humans and Mice 
PURPOSE
An osteopontin (OPN; SPP1) gene promoter polymorphism modifies disease severity in Duchenne muscular dystrophy, and we hypothesized that it might also modify muscle phenotypes in healthy volunteers.
METHODS
Gene association studies were carried out for OPN (rs28357094) in the FAMuSS cohort (n=752; age 23.7±5.7 yrs). Phenotypes studied included muscle size (MRI), strength, and response to supervised resistance training. We also studied 147 young adults that had carried out a bout of eccentric elbow exercise (age 24.0 ± 5.2 yrs). Phenotypes analyzed included strength, soreness, and serum muscle enzymes.
RESULTS
In the FAMuSS cohort, the G allele was associated with 17% increase in baseline upper arm muscle volume only in women (F=26.32; p=5.32 × 10−7), explaining 5% of population variance. In the eccentric damage cohort, weak associations of the G allele were seen in women with both baseline myoglobin, and elevated CK. Sexually dimorphic effects of OPN on muscle were also seen in OPN null mice. Five of seven muscle groups examined showed smaller size in OPN null female mice, whereas two were smaller in males. Query of OPN gene transcription after experimental muscle damage in mice showed rapid induction within 12 hrs (100-fold increase from baseline), followed by sustained high level expression through 16 days of regeneration before falling to back to baseline.
CONCLUSION
OPN is a sexually dimorphic modifier of muscle size in normal humans and mice, and responds to muscle damage. The OPN gene is known to be estrogen responsive, and this may explain the female-specific genotype effects in adult volunteers.
doi:10.1249/MSS.0b013e31828093c1
PMCID: PMC3631433  PMID: 23274598
osteopontin (OPN); secreted phosphoprotein 1 (SPP1); genetic polymorphism; estrogen; hypertrophy; MRI
7.  Natural Progression of Childhood Asthma Symptoms and Strong Influence of Sex and Puberty 
Rationale: Asthma prevalence, onset, remission and relapse, and healthcare use have been intensively studied. However, asthma symptom progression through childhood and adolescence has not been well studied, in part due to the challenges in obtaining consistent and robust long-term follow-up data on a large series of subjects with asthma.
Objectives: To use the asthma diary symptom data of the Childhood Asthma Management Program placebo group (5 yr, 418 subjects, and total 564,518 records) to establish sex-specific high-resolution time courses of the natural progression of asthma symptoms through childhood and adolescence.
Methods: We used the asthma diary symptom code as a measure of daily disease severity. Annual records of Tanner stage were used to determine the influence of puberty on severity. A data alignment technique was used to derive 13-year time courses of mean symptoms and mean Tanner stage.
Measurements and Main Results: Data analyses showed three age- and sex-related phases of asthma symptom progression: Phase 1 (ages 5 and 6 yr)—greater severity in boys; Phase 2 (ages 7 to 9 yr)—no sex difference in severity; and Phase 3 (age 10-17 yr)—greater severity in girls. The continuous decline of symptoms in both sexes stops abruptly at the onset of puberty.
Conclusions: The severity of asthma symptoms varies through childhood and adolescence, and patterns differ by sex. Puberty has a strong influence on symptom progression in both sexes. Progression of symptoms is a distinct aspect of asthma epidemiology.
doi:10.1513/AnnalsATS.201402-084OC
PMCID: PMC4213994  PMID: 24896645
epidemiology; sex difference; sex dominance
8.  The ACTN3 R577X Polymorphism Is Associated with Cardiometabolic Fitness in Healthy Young Adults 
PLoS ONE  2015;10(6):e0130644.
Homozygosity for a premature stop codon (X) in the ACTN3 “sprinter” gene is common in humans despite the fact that it reduces muscle size, strength and power. Because of the close relationship between skeletal muscle function and cardiometabolic health we examined the influence of ACTN3 R577X polymorphism over cardiovascular and metabolic characteristics of young adults (n = 98 males, n = 102 females; 23 ± 4.2 years) from our Assessing Inherent Markers for Metabolic syndrome in the Young (AIMMY) study. Both males and females with the RR vs XX genotype achieved higher mean VO2 peak scores (47.8 ± 1.5 vs 43.2 ±1.8 ml/O2/min, p = 0.002) and exhibited higher resting systolic (115 ± 2 vs 105 ± mmHg, p = 0.027) and diastolic (69 ± 3 vs 59 ± 3 mmHg, p = 0.005) blood pressure suggesting a role for ACTN3 in the maintenance of vascular tone. We subsequently identified the expression of alpha-actinin 3 protein in pulmonary artery smooth muscle, which may explain the genotype-specific differences in cardiovascular adaptation to acute exercise. In addition, we utilized targeted serum metabolomics to distinguish between RR and XX genotypes, suggesting an additional role for the ACTN3 R577X polymorphism in human metabolism. Taken together, these results identify significant cardiometabolic effects associated with possessing one or more functional copies of the ACTN3 gene.
doi:10.1371/journal.pone.0130644
PMCID: PMC4480966  PMID: 26107372
9.  Exon-skipping Therapy for Muscular Dystrophy: A Roadblock, Detour, or Bump in the Road? 
Science translational medicine  2014;6(230):230fs14.
Duchenne muscular dystrophy (DMD) affects 1in 5,000 newborn males. These boys appear healthy as infants and young children, but then experience a heartbreaking decline, as muscle tissue gradually wastes away, leaving patients nonambulant by their late teens. The heart and respiratory muscles are similarly weakened, compromising life span. DMD has served as a test bed for population genetics in the 1950’s, gene identification methods (reverse genetics) in the 1980’s, and the integration of molecular diagnostics into patient diagnosis and family counseling. Additional landmarks are held by the dystrophin gene: It is the largest in the human genome—2.3 million base pairs—and has the highest known spontaneous mutation rate of all human genes. Although we have made robust progress in understanding the molecular basis of DMD, translation of these advances to improvements in patient care has been painfully slow. Early hints of success with stem cell transplantation and replacement gene therapy hit technical roadblocks of delivery and immunological barriers that have remained persistently impassable.
doi:10.1126/scitranslmed.3008873
PMCID: PMC4464785  PMID: 24695683
10.  VBP15, a Glucocorticoid Analogue, Is Effective at Reducing Allergic Lung Inflammation in Mice 
PLoS ONE  2013;8(5):e63871.
Asthma is a chronic inflammatory condition of the lower respiratory tract associated with airway hyperreactivity and mucus obstruction in which a majority of cases are due to an allergic response to environmental allergens. Glucocorticoids such as prednisone have been standard treatment for many inflammatory diseases for the past 60 years. However, despite their effectiveness, long-term treatment is often limited by adverse side effects believed to be caused by glucocorticoid receptor-mediated gene transcription. This has led to the pursuit of compounds that retain the anti-inflammatory properties yet lack the adverse side effects associated with traditional glucocorticoids. We have developed a novel series of steroidal analogues (VBP compounds) that have been previously shown to maintain anti-inflammatory properties such as NFκB-inhibition without inducing glucocorticoid receptor-mediated gene transcription. This study was undertaken to determine the effectiveness of the lead compound, VBP15, in a mouse model of allergic lung inflammation. We show that VBP15 is as effective as the traditional glucocorticoid, prednisolone, at reducing three major hallmarks of lung inflammation—NFκB activity, leukocyte degranulation, and pro-inflammatory cytokine release from human bronchial epithelial cells obtained from patients with asthma. Moreover, we found that VBP15 is capable of reducing inflammation of the lung in vivo to an extent similar to that of prednisone. We found that prednisolone–but not VBP15 shortens the tibia in mice upon a 5 week treatment regimen suggesting effective dissociation of side effects from efficacy. These findings suggest that VBP15 may represent a potent and safer alternative to traditional glucocorticoids in the treatment of asthma and other inflammatory diseases.
doi:10.1371/journal.pone.0063871
PMCID: PMC3646769  PMID: 23667681
11.  The 1p13.3 LDL (C)-Associated Locus Shows Large Effect Sizes in Young Populations 
Pediatric research  2011;69(6):538-543.
Genome-wide association studies (GWAS) have identified polymorphic loci associated with coronary artery disease (CAD) risk factors (i. e. serum lipids) in adult populations (42–69 yrs). We hypothesized that younger populations would show a greater relative genetic component due to fewer confounding variables. We examined the influence of 20 GWAS loci associated with serum lipids and insulin metabolism, in a university student cohort (n=548; mean age= 24 yrs), and replicated statistically associated results in a second study cohort of primary school students (n=810, mean age= 11.5 yrs). 19 loci showed no relationship with studied risk factors in young adults. However, the ancestral allele of the rs646776 (SORT1) locus was strongly associated with increased low density lipoprotein cholesterol {LDL (C)} in young adults (TT: 97.6 ± 1.0 mg/dL {n=345}, vs. CT/CC: 87.3 ± 1.0 mg/dL {n=203}; p = 3 × 10−6) and children (TT: 94.0 ± 1.3 mg/dL {n=551}, vs. CT/CC: 84.7 ± 1.4 mg/dL {n=259}; p = 4 × 10−6). This locus is responsible for 3.6% of population variance in young adults and 2.5% of population variance in children. The effect size of the SORT1 locus is considerably higher in young populations (2.5%–4.1%) compared to older subjects (1%).
doi:10.1203/PDR.0b013e3182139227
PMCID: PMC3606915  PMID: 21297524
12.  Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia 
Journal of Clinical Microbiology  2014;52(11):3913-3921.
In critically ill patients, the development of pneumonia results in significant morbidity and mortality and additional health care costs. The accurate and rapid identification of the microbial pathogens in patients with pulmonary infections might lead to targeted antimicrobial therapy with potentially fewer adverse effects and lower costs. Major advances in next-generation sequencing (NGS) allow culture-independent identification of pathogens. The present study used NGS of essentially full-length PCR-amplified 16S ribosomal DNA from the bronchial aspirates of intubated patients with suspected pneumonia. The results from 61 patients demonstrated that sufficient DNA was obtained from 72% of samples, 44% of which (27 samples) yielded PCR amplimers suitable for NGS. Out of the 27 sequenced samples, only 20 had bacterial culture growth, while the microbiological and NGS identification of bacteria coincided in 17 (85%) of these samples. Despite the lack of bacterial growth in 7 samples that yielded amplimers and were sequenced, the NGS identified a number of bacterial species in these samples. Overall, a significant diversity of bacterial species was identified from the same genus as the predominant cultured pathogens. The numbers of NGS-identifiable bacterial genera were consistently higher than identified by standard microbiological methods. As technical advances reduce the processing and sequencing times, NGS-based methods will ultimately be able to provide clinicians with rapid, precise, culture-independent identification of bacterial, fungal, and viral pathogens and their antimicrobial sensitivity profiles.
doi:10.1128/JCM.01678-14
PMCID: PMC4313225  PMID: 25143582
13.  Genetic modifiers of ambulation in the cooperative international Neuromuscular research group Duchenne natural history study 
Annals of Neurology  2015;77(4):684-696.
Objective
We studied the effects of LTBP4 and SPP1 polymorphisms on age at loss of ambulation (LoA) in a multiethnic Duchenne muscular dystrophy (DMD) cohort.
Methods
We genotyped SPP1 rs28357094 and LTBP4 haplotype in 283 of 340 participants in the Cooperative International Neuromuscular Research Group Duchenne Natural History Study (CINRG-DNHS). Median ages at LoA were compared by Kaplan–Meier analysis and log-rank test. We controlled polymorphism analyses for concurrent effects of glucocorticoid corticosteroid (GC) treatment (time-varying Cox regression) and for population stratification (multidimensional scaling of genome-wide markers).
Results
Hispanic and South Asian participants (n = 18, 41) lost ambulation 2.7 and 2 years earlier than Caucasian subjects (p = 0.003, <0.001). The TG/GG genotype at SPP1 rs28357094 was associated to 1.2-year-earlier median LoA (p = 0.048). This difference was greater (1.9 years, p = 0.038) in GC-treated participants, whereas no difference was observed in untreated subjects. Cox regression confirmed a significant effect of SPP1 genotype in GC-treated participants (hazard ratio = 1.61, p = 0.016). LTBP4 genotype showed a direction of association with age at LoA as previously reported, but it was not statistically significant. After controlling for population stratification, we confirmed a strong effect of LTBP4 genotype in Caucasians (2.4 years, p = 0.024). Median age at LoA with the protective LTBP4 genotype in this cohort was 15.0 years, 16.0 for those who were treated with GC.
Interpretation
SPP1 rs28357094 acts as a pharmacodynamic biomarker of GC response, and LTBP4 haplotype modifies age at LoA in the CINRG-DNHS cohort. Adjustment for GC treatment and population stratification appears crucial in assessing genetic modifiers in DMD.
doi:10.1002/ana.24370
PMCID: PMC4403971  PMID: 25641372
14.  Evolution and comparative genomics of subcellular specializations: EST sequencing of Torpedo electric organ 
Marine genomics  2011;4(1):33-40.
Uncharacterized open reading frames (ORFs) in human genomic sequence often show a high degree of evolutionary conservation, yet have little or no tissue EST or protein data suggestive of protein product function. The encoded proteins may have highly restricted expression in specialized cells, subcellular specializations, and/or narrow windows during development. One such highly specialized and minute subcellular compartment is the neuromuscular junction (NMJ), where motorneurons contact muscle fibers. The electric Torpedo ray has evolved to expand the NMJ structure to the size of a large organ (electroplax organ), and we hypothesized that Torpedo electroplax proteins would be candidates for human ESTs expressed at the human NMJ. A total of 9,719 primary electroplax cDNA clones were sequenced. We identified 44 human ORFs showing high (>63%) amino acid identity to Torpedo electroplax transcripts with enrichment for mRNA splicing motifs (SH2 and pre-mRNA splicing domains), an observation potentially important for the strict nuclear domains maintained by myonuclei underlying the NMJ. We generated antibodies against two uncharacterized human genes (C19orf29 [Drosophila cactin] and C15orf24) and showed that these were indeed expressed at the murine NMJ. Cactin, a member of the Rel transcription factor family in Drosophila, localized to the postsynaptic cytosol of the NMJ and nuclear membrane. C15orf24 protein localized to the murine postsynaptic sarcolemma. We show a novel approach towards identifying proteins expressed at a subcellular specializations using evolutionary diversity of organ function and cross-species mapping.
doi:10.1016/j.margen.2010.12.004
PMCID: PMC3412124  PMID: 21429463
Electric organ; Neuromuscular Junction (NMJ); Proteome; Torpedo californica; Novel Gene Discovery; Open Reading Frame (ORF)
15.  An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss 
Genome Biology  2015;16(1):8.
Background
Environmental factors can influence obesity by epigenetic mechanisms. Adipose tissue plays a key role in obesity-related metabolic dysfunction, and gastric bypass provides a model to investigate obesity and weight loss in humans.
Results
Here, we investigate DNA methylation in adipose tissue from obese women before and after gastric bypass and significant weight loss. In total, 485,577 CpG sites were profiled in matched, before and after weight loss, subcutaneous and omental adipose tissue. A paired analysis revealed significant differential methylation in omental and subcutaneous adipose tissue. A greater proportion of CpGs are hypermethylated before weight loss and increased methylation is observed in the 3′ untranslated region and gene bodies relative to promoter regions. Differential methylation is found within genes associated with obesity, epigenetic regulation and development, such as CETP, FOXP2, HDAC4, DNMT3B, KCNQ1 and HOX clusters. We identify robust correlations between changes in methylation and clinical trait, including associations between fasting glucose and HDAC4, SLC37A3 and DENND1C in subcutaneous adipose. Genes investigated with differential promoter methylation all show significantly different levels of mRNA before and after gastric bypass.
Conclusions
This is the first study reporting global DNA methylation profiling of adipose tissue before and after gastric bypass and associated weight loss. It provides a strong basis for future work and offers additional evidence for the role of DNA methylation of adipose tissue in obesity.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0569-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-014-0569-x
PMCID: PMC4301800  PMID: 25651499
16.  Elevated stearoyl-CoA desaturase-1 expression in skeletal muscle contributes to abnormal fatty acid partitioning in obese humans 
Cell metabolism  2005;2(4):251-261.
Summary
Obesity and type 2 diabetes are strongly associated with abnormal lipid metabolism and accumulation of intramyocellular triacylglycerol, but the underlying cause of these perturbations are yet unknown. Herein, we show that the lipogenic gene, stearoyl-CoA desaturase 1 (SCD1), is robustly up-regulated in skeletal muscle from extremely obese humans. High expression and activity of SCD1, an enzyme that catalyzes the synthesis of monounsaturated fatty acids, corresponded with low rates of fatty acid oxidation, increased triacylglycerol synthesis and increased monounsaturation of muscle lipids. Elevated SCD1 expression and abnormal lipid partitioning were retained in primary skeletal myocytes derived from obese compared to lean donors, implying that these traits might be driven by epigenetic and/or heritable mechanisms. Overexpression of human SCD1 in myotubes from lean subjects was sufficient to mimic the obese phenotype. These results suggest that elevated expression of SCD1 in skeletal muscle contributes to abnormal lipid metabolism and progression of obesity.
doi:10.1016/j.cmet.2005.09.002
PMCID: PMC4285571  PMID: 16213227
17.  Neck and waist circumference biomarkers of cardiovascular risk in a cohort of predominantly African-American college students: A preliminary study 
doi:10.1016/j.jand.2013.07.005
PMCID: PMC4038263  PMID: 24051106
African Americans; anthropometry; blood pressure; body fat; health risk appraisal; low density lipoprotein cholesterol; students; waist-hip ratio
18.  Non-Invasive MRI and Spectroscopy of mdx Mice Reveal Temporal Changes in Dystrophic Muscle Imaging and in Energy Deficits 
PLoS ONE  2014;9(11):e112477.
In Duchenne muscular dystrophy (DMD), a genetic disruption of dystrophin protein expression results in repeated muscle injury and chronic inflammation. Magnetic resonance imaging shows promise as a surrogate outcome measure in both DMD and rehabilitation medicine that is capable of predicting clinical benefit years in advance of functional outcome measures. The mdx mouse reproduces the dystrophin deficiency that causes DMD and is routinely used for preclinical drug testing. There is a need to develop sensitive, non-invasive outcome measures in the mdx model that can be readily translatable to human clinical trials. Here we report the use of magnetic resonance imaging and spectroscopy techniques for the non-invasive monitoring of muscle damage in mdx mice. Using these techniques, we studied dystrophic mdx muscle in mice from 6 to 12 weeks of age, examining both the peak disease phase and natural recovery phase of the mdx disease course. T2 and fat-suppressed imaging revealed significant levels of tissue with elevated signal intensity in mdx hindlimb muscles at all ages; spectroscopy revealed a significant deficiency of energy metabolites in 6-week-old mdx mice. As the mdx mice progressed from the peak disease stage to the recovery stage of disease, each of these phenotypes was either eliminated or reduced, and the cross-sectional area of the mdx muscle was significantly increased when compared to that of wild-type mice. Histology indicates that hyper-intense MRI foci correspond to areas of dystrophic lesions containing inflammation as well as regenerating, degenerating and hypertrophied myofibers. Statistical sample size calculations provide several robust measures with the ability to detect intervention effects using small numbers of animals. These data establish a framework for further imaging or preclinical studies, and they support the development of MRI as a sensitive, non-invasive outcome measure for muscular dystrophy.
doi:10.1371/journal.pone.0112477
PMCID: PMC4229202  PMID: 25390038
19.  Progression of volume load and muscular adaptation during resistance exercise 
European journal of applied physiology  2010;111(6):1063-1071.
Volume load (VL) is suggested to influence the adaptation of muscle to resistance exercise (RE). We sought to examine the independent association between total VL and hypertrophy and strength following a progressive RE protocol of equated sets and intensity. Total VL was calculated in 83 subjects (n = 43 males, n = 40 females; age = 25.12 ± 5.5 years) who participated in unilateral arm RE for 12 weeks. Subjects were tested for biceps muscle volume (MRI of the upper arm), isometric maximal voluntary contraction (MVC), and dynamic biceps strength (1RM), at baseline and following RE. Linear regression analysis revealed that sex was a significant predictor of hypertrophy (β = 0.06; p = 0.01) and strength (β = 0.14; p = 0.04), and that males had greater increases. Total VL was independently associated with hypertrophy only among females (β = 0.12; p < 0.01). For males, only baseline strength was (inversely) related to hypertrophy (β = −0.12; p = 0.04). VL was strongly associated with changes in 1RM strength improvement for both males (β = 0.66; p < 0.01) and females (β = 0.26; p = 0.02), but only related to MVC among females (β = 0.20; p = 0.02). Findings reveal that VL was independently associated with hypertrophy only among females. For males baseline strength was independently and inversely related to changes in muscle mass. Conversely, VL was found to be strongly associated with changes in 1RM for both males and females, controlling for age, body mass, and baseline strength.
doi:10.1007/s00421-010-1735-9
PMCID: PMC4215195  PMID: 21113614
Strength training; Volume load; FAMuSS; Muscle mass; Periodization
20.  Mathematical Modeling of Corticosteroid Pharmacogenomics in Rat Muscle following Acute and Chronic Methylprednisolone Dosing 
Molecular pharmaceutics  2008;5(2):328-339.
The pharmacogenomic effects of a corticosteroid (CS) were assessed in rat skeletal muscle using microarrays. Adrenalectomized (ADX) rats were treated with methylprednisolone (MPL) by either 50 mg/kg intravenous injection or 7-day 0.3 mg/kg/h infusion through subcutaneously implanted pumps. RNAs extracted from individual rat muscles were hybridized to Affymetrix Rat Genome Genechips. Data mining yielded 653 and 2316 CS-responsive probe sets following MPL bolus and infusion treatments. Of these, 196 genes were controlled by MPL under both dosing conditions. Cluster analysis revealed that 124 probe sets exhibited three typical expression dynamic profiles following acute dosing. Cluster A consisted of up-regulated probe sets which were grouped into five subclusters each exhibiting unique temporal patterns during the infusion. Cluster B comprised down-regulated probe sets which were divided into two subclusters with distinct dynamics during the infusion. Cluster C probe sets exhibited delayed down-regulation under both bolus and infusion conditions. Among those, 104 probe sets were further grouped into subclusters based on their profiles following chronic MPL dosing. Several mathematical models were proposed and adequately captured the temporal patterns for each subcluster. Multiple types of dosing regimens are needed to resolve common determinants of gene regulation as chronic exposure results in unexpected differences in gene expression compared to acute dosing. Pharmacokinetic/pharmacodynamic (PK/PD) modeling provides a quantitative tool for elucidating the complexities of CS pharmacogenomics in skeletal muscle.
doi:10.1021/mp700094s
PMCID: PMC4196382  PMID: 18271548
Microarray studies; pharmacokinetics; pharmacodynamics; mathematical models; computational biology
21.  Microarray analysis of the temporal response of skeletal muscle to methylprednisolone: comparative analysis of two dosing regimens 
Physiological genomics  2007;30(3):282-299.
The transcriptional response of skeletal muscle to chronic corticosteroid exposure was examined over 168 h and compared with the response profiles observed following a single dose of corticosteroid. Male adrenalectomized Wistar rats were given a constant-rate infusion of 0.3 mg•kg−1•h−1 methylprednisolone for up to 7 days via subcutaneously implanted minipumps. Four control and forty drug-treated animals were killed at ten different time points during infusion. Liver total RNAs were hybridized to 44 individual Affymetrix REA230A gene chips. Previously, we described a filtration approach for identifying genes of interest in microarray data sets developed from tissues of rats treated with methylprednisolone (MPL) following acute dosing. Here, a similar approach involving a series of three filters was applied sequentially to identify genes of interest. These filters were designed to eliminate probe sets that were not expressed in the tissue, not regulated by the drug, or did not meet defined quality control standards. Filtering eliminated 86% of probe sets, leaving a remainder of 2,316 for further consideration. In a previous study, 653 probe sets were identified as MPL regulated following administration of a single (acute) dose of the drug. Comparison of the two data sets yielded 196 genes identified as regulated by MPL in both dosing regimens. Because of receptor downregulation, it was predicted that genes regulated by receptor-glucocorticoid response element interactions would exhibit tolerance in chronic profiles. However, many genes did not exhibit steroid tolerance, indicating that present perspectives on the mechanism of glucocorticoid action cannot entirely explain all temporal profiles.
doi:10.1152/physiolgenomics.00242.2006
PMCID: PMC4186702  PMID: 17473217
glucocorticoids; corticosteroids; Affymetrix gene chips; gene expression; time series
23.  Application of Scaling Factors in Simultaneous Modeling of Microarray Data from Diverse Chips 
Pharmaceutical research  2007;24(4):643-649.
Purpose
Microarrays have been utilized in many biological, physiological and pharmacological studies as a high-throughput genomic technique. Several generations of Affymetrix GeneChip® microarrays are widely used in gene expression studies. However, differences in intensities of signals for different probe sets that represent the same gene on various types of Affymetrix chips make comparison of datasets complicated.
Materials and Methods
A power coefficient scaling factor was applied in the pharmacokinetic/ pharmacodynamic (PK/PD) modeling to account for differences in probe set sensitivities (i.e., signal intensities). Microarray data from muscle and liver following methylprednisolone 50 mg/kg i.v. bolus and 0.3 mg/kg/h infusion regimens were taken as an exemplar.
Results
The scaling factor applied to the pharmacodynamic output function was used to solve the problem of intensity differences between probe sets. This approach yielded consistent pharmacodynamic parameters for the applied models.
Conclusions
Modeling of pharmacodynamic/pharmacogenomic (PD/PG) data from diverse chips should be performed with caution due to differential probe set intensities. In such circumstances, a power scaling factor can be applied in the modeling.
doi:10.1007/s11095-006-9215-y
PMCID: PMC4181592  PMID: 17318415
bioinformatics; computational biology; pharmacodynamics; pharmacogenomics; pharmacokinetics
24.  Time Series Proteome Profiling To Study Endoplasmic Reticulum Stress Response 
Journal of proteome research  2008;7(6):2435-2444.
Time series profiling is a powerful approach for obtaining information on protein expression dynamics and prevailing biochemical pathways. To date, such information could only be obtained at the mRNA level using mature and highly parallel technologies such as microarray gene expression profiling. The generation of time series data at the protein level has lagged due to the lack of robust and highly reproducible methodologies. Using a combination of SILAC strategy, SDS-PAGE and LC-MS/MS, we demonstrate successful monitoring of expression levels of the same set of proteins across different time points within the ER compartment of human primary fibroblast cells when exposed to ER stress inducers tunicamycin and thapsigargin. Data visualization was facilitated using GeneSpring GX analysis platform that was designed to process Affymetrix microarray data. This software also facilitated the generation of important parameters such as data normalization, calculation of statistical values to extract significant changes in protein expression, and the cross comparison of data sets.
doi:10.1021/pr700842m
PMCID: PMC4154506  PMID: 18435558
SILAC; Isotope Ratio; LC-MS/MS; Proteome profiling; Time series; ER stress; GRP78; Reticulocalbin
25.  Microarray Analysis Reveals Novel Features of the Muscle Aging Process in Men and Women 
To develop a global view of muscle transcriptional differences between older men and women and sex-specific aging, we obtained muscle biopsies from the biceps brachii of young and older men and women and profiled the whole-genome gene expression using microarray. A logistic regression-based method in combination with an intensity-based Bayesian moderated t test was used to identify significant sex- and aging-related gene functional groups. Our analysis revealed extensive sex differences in the muscle transcriptome of older individuals and different patterns of transcriptional changes with aging in men and women. In older women, we observed a coordinated transcriptional upregulation of immune activation, extracellular matrix remodeling, and lipids storage; and a downregulation of mitochondrial biogenesis and function and muscle regeneration. The effect of aging results in sexual dimorphic alterations in the skeletal muscle transcriptome, which may modify the risk for developing musculoskeletal and metabolic diseases in men and women.
doi:10.1093/gerona/glt015
PMCID: PMC3826860  PMID: 23418191
Aging; Sex; Sarcopenia; Transcription profile.

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