Changes In mRNA Expression Of Genes Research Articles

Predicting the Long-Term Effects of Therapeutic Neutralization of Oncostatin M on Human Hematopoiesis.

Therapeutic neutralization of Oncostatin M (OSM) causes mechanism-driven anemia and thrombocytopenia, which narrows the therapeutic window complicating the selection of doses (and dosing intervals) that optimize efficacy and safety. We utilized clinical data from studies of an anti-OSM monoclonal antibody (GSK2330811) in healthy volunteers (n = 49) and systemic sclerosis patients (n = 35), to quantitatively determine the link between OSM and alterations in red blood cell (RBC) and platelet production. Longitudinal changes in hematopoietic variables (including RBCs, reticulocytes, platelets, erythropoietin, and thrombopoietin) were linked in a physiology-based model, to capture the long-term effects and variability of therapeutic OSM neutralization on human hematopoiesis. Free serum OSM stimulated precursor cell production through sigmoidal relations, with higher maximum suppression (Imax ) and OSM concentration for 50% suppression (IC50 ) for platelets (89.1% [95% confidence interval: 83.4-93.0], 6.03 pg/mL [4.41-8.26]) than RBCs (57.0% [49.7-64.0], 2.93 pg/mL [2.55-3.36]). Reduction in hemoglobin and platelets increased erythro- and thrombopoietin, respectively, prompting reticulocytosis and (partially) alleviating OSM-restricted hematopoiesis. The physiology-based model was substantiated by preclinical data and utilized in exploration of once-weekly or every other week dosing regimens. Predictions revealed an (for the indication) unacceptable occurrence of grade 2 (67% [58-76], 29% [20-38]) and grade 3 (17% [10-25], 3% [0-7]) anemias, with limited thrombocytopenia. Individual extent of RBC precursor modulation was moderately correlated to skin mRNA gene expression changes. The physiological basis and consideration of interplay among hematopoietic variables makes the model generalizable to other drug and nondrug scenarios, with adaptations for patient populations, diseases, and therapeutics that modulate hematopoiesis or exhibit risk of anemia and/or thrombocytopenia.

Identification of Candidate mRNA Genes and Their Potential MicroRNA Targets in Lung Cancer Induced by Smoking Tobacco.

Smoking is considered the single highest risk factor for lung cancer and has been suggested to be associated with accelerated somatic mutations in respiratory mucosa that lead to the development of lung cancer. MicroRNAs serve as modulators in smoking-induced mRNA gene expression changes in the human airway epithelium and are linked to the development of lung cancer. The thermodynamics in the microRNA (miRNA)-mRNA interactions may be affected in tobacco smokers, consequently, leading to phenotypic variations in lung cancer patients. Therefore, this study aimed to investigate the impact of smoking tobacco on somatic mutations in mRNA genes and assess their potential impact on miRNA-mRNA interactions in lung cancers. The clinically significant pathogenic variants in mRNA genes in the dataset in lung cancer cases linked to smoking tobacco (n = 330) were obtained from the Cancer Atlas database (TCGA, http://cancergenome.nih.gov/) and used to assess the potential role of tobacco consumption in driving the genetic alterations in proto-oncogenes associated with lung cancer. The analysis of the miRNA interaction with the top five altered mRNA proto-oncogenes in lung cancer cases due to tobacco consumption was performed using the target prediction function in the miRDP program (Database version 5.2.3.1, https://mirdb.org/). We identified the top five mRNA proto-oncogenes enriched with simple somatic mutations (SSM) in lung cancer were TP53, EGFR, KRAS, FAT4, and KMT2D. Interestingly, we observed the highest incidence of SSM in the Tumor Protein p53 (TP53) gene at 63.64%. Similarly, the SSM incidence was 23.94% in the Epidermal Growth Factor Receptor (EGFR), 22.12% in the Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS), 18.48% in the FAT Atypical Cadherin 4 (FAT4), and 14.24% in the Lysine (K)-Specific Methyltransferase 2D (KMT2D) genes. Subsequently, we used a bioinformatics approach to assess the effect of miRNA-mRNA interactions in lung cancer among the top five SSM-enriched mRNA proto-oncogenes. Among the top 20 identified and selected miRNAs, we observed 18 unique microRNAs that bind specifically to TP53, KRAS, and FAT4 genes and 17 and 19 microRNAs that exclusively bind with the EGFR and KMT2D genes, respectively. Our study found that the top five SSM-enriched mRNA proto-oncogenes in lung cancers among tobacco smokers were TP53, EGFR, KRAS, FAT4, and KMT2D. Further, our results provide an important insight into the involvement of the intricate network of mRNA-miRNA interactions in the development of lung cancer.

Whole transcriptome analysis in offspring whose fathers were exposed to a developmental insult: a novel avian model

Although the effects of paternal exposure to insults on the offspring received limited attention in the past, it is currently gaining interest especially after understanding the mechanisms which may mediate such exposure effects. In the current study, the well-controlled avian model (Fayoumi) was utilized to investigate the effects of paternal exposure to the developmental insult, chlorpyrifos on the offspring’s gene expression via mRNA and small RNA sequencing. Numerous mRNA gene expression changes were detected in the offspring after paternal exposure to the developmental insult, especially in genes related to neurogenesis, learning and memory. qPCR analysis of several genes, that were significantly changed in mRNA sequencing, confirmed the results obtained in mRNA sequencing. On the other hand, small RNA sequencing did not identify significant microRNA genes expression changes in the offspring after paternal exposure to the developmental insult. The effects of the paternal exposure were more pronounced in the female offspring compared to the male offspring. The results identified expression alterations in major genes (some of which were pertinent to the functional changes observed in other forms of early developmental exposure) after paternal insult exposure and provided a direction for future studies involving the most affected genes.

Persistent organic pollutant exposure and associations with gene expression in northern fur seals (Callorhinus ursinus) from St. Paul Island, Alaska

Persistent organic pollutants (POPs) are highly lipophilic compounds that accumulate at increased concentrations in high tropic level organisms like marine mammals. Marine mammals’ reliance on blubber makes them susceptible to accumulating POPs at potentially toxic concentrations. In this study, we analyzed POP concentrations, (polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), polybrominated diphenyl ethers (PBDEs), and methoxylated-BDE (MeOBDE), in the blubber of 16 subsistence harvested sub-adult, male northern fur seals as well as assessed changes in mRNA gene expression of nine relevant biomarkers including the aryl hydrocarbon receptor, thyroid receptor-α, and adiponectin. PBDE and MeOBDE concentrations were significantly lower than PCB and OCP concentrations. A negative relationship was observed between percent lipid in the blubber and contaminant concentrations, both individual and sum. Expression changes in eight biomarkers were correlated with individual and sum contaminant concentrations. This study shows that contaminant concentrations measured are correlated to changes in expression of genes from different physiological systems, metabolism and endocrine, that are important for the regulation of blubber metabolism. Northern fur seals are reliant on blubber as an energy source during times of low food intake. Potential contaminant induced changes in blubber metabolism pathways could have significant impacts on the health of individuals during critical periods.

Machine learning algorithm selects transcripts in blood to distinguish Alzheimer’s disease and other neurodegenerative diseases

AbstractBackgroundClinical diagnosis of neurodegenerative diseases is notoriously inaccurate and current methods are often expensive, time‐consuming, or invasive. Simple inexpensive and noninvasive methods of diagnosis could provide valuable support for clinicians when combined with cognitive assessment scores thereby reducing health care costs by ruling out or streamlining additional tests such as imaging. Biological processes leading to neuropathology are reflected in both the central nervous system and vascular peripheral system and progress silently for many years. Because Alzheimer’s disease (AD) symptoms often overlap with common disorders that may be treatable or reversible, an accurate diagnosis at the earliest time is crucial. A blood‐based screen to distinguish and classify neurodegenerative diseases is especially interesting having low cost, minimal invasiveness, and accessibility to almost any world clinic. Additionally, an inexpensive blood panel could also monitor disease progression, for example, marking the advancement beyond mild cognitive impairment (MCI).MethodThe study of blood‐based changes in mRNA gene expression presents a good strategy for differentiating patients of any neurodegenerative disease regardless of the proteins or their post‐translational modifications occurring in disease. Information about features selected for the classification may also guide insight into possible treatment strategies. Using existing public datasets, we developed a machine learning algorithm for application on transcripts present in blood.ResultOur machine learning algorithm generated small sets of transcripts which distinguish a number of neurodegenerative diseases with high sensitivity and specificity.ConclusionNeurodegenerative diseases such as AD are associated with changes in specific molecular pathways and signatures. Using RNA expression as blood biomarkers can also provide information for a pathophysiological relationship with disease and gives us the advantage of using the vast knowledge of gene expression to not only predict disease but also analyze the pathways involved. Our chosen transcripts reveal that neurodegenerative diseases have common themes which after removal bare the unique transcripts of each disease.

Acute restraint stress does not alter corticosteroid receptors or 11β-hydroxysteroid dehydrogenase gene expression at hypothalamic–pituitary-adrenal axis regulatory sites in captive male white-crowned sparrows (Zonotrichia leucophrys gambelii)

Capture-restraint is often used to investigate the acute hypothalamic–pituitary-adrenal axis (HPA) response to stress in wild and captive animals through the production of glucocorticoids. Although this approach is useful for understanding changes in glucocorticoids, it overlooks potential changes in the complex regulatory systems associated with the glucocorticoid response, including genomic receptors, steroid metabolizing enzymes, carrier proteins, and downstream target proteins (e.g. gonadotropin-inhibitory hormone; GnIH). The present study in captive male white-crowned sparrows (Zonotrichia leucophrys) tests the hypothesis that corticosteroid receptors (mineralocorticoid - MR and glucocorticoid - GR), 11β-hydroxysteroid dehydrogenase 1 (11βHSD1) and 2 (11βHSD2), corticosteroid binding globulin (CBG), and GnIH undergo rapid changes in expression to mediate the glucocorticoid response to acute stress. To determine dynamic changes in gene mRNA expression in the hippocampus, hypothalamus, pituitary gland, and liver, birds were sampled within 3 min of entering the room and after 10, 30, and 60 min of capture restraint stress in a cloth bag. Restraint stress handling increased CBG and decreased GnIH mRNA expression in the liver and hypothalamus, respectively. MR, GR, 11βHSD1, and 11βHSD2 mRNA expression in the brain, pituitary gland, and liver did not change. No correlations were found between gene expression and baseline or stress-induced plasma corticosterone levels. No rapid changes of MR, GR, 11βHSD1, and 11βHSD2 mRNA expression during a standardized acute restraint protocol suggests that tissue level sensitivity may remain constant during acute stressors. However, the observed rise in CBG mRNA expression could act to facilitate transport to target tissues or buffer the rise in circulating glucocorticoids. Further studies on tissue specific sensitivity are warranted.

Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) disrupts zebrafish tail fin development

The flame retardant, tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), is one of the most developmentally toxic organophosphate flame retardants (OPFRs). However, few mechanistic studies on phenotypic malformation caused by TDCIPP have been conducted. This study investigates the molecular mechanism underlying abnormal tail fin development consistently observed in zebrafish embryos exposed to TDCIPP. The results show that the defects in the tail fin (e.g., bent spine, defective caudal fin, and damaged tip) were associated with altered expression of transcription factors. The significant up-regulation of mmp9 and, among insulin-growth factor (IGF) families, igfbp-1a and igfbp1b was observed, whereas alterations in the expression of cdx4, igf1a, ifg1b, igf2b, and vegaa regulating tail development were dependent on time points. In accordance with changes in mRNA gene expression, TDCIPP impaired vessel formation and disorganized muscle in transgenic Tg(fli-GFP) zebrafish larvae. Furthermore, we found that the overexpression of mmp9 caused by TDCIPP was not linked to igfbp-1. Overall, these findings demonstrate that TDCIPP disrupts the progression of tail fin development, accompanied by defects in vessel and muscle formation in developing zebrafish embryos.

Reduced mitochondrial reactive oxygen species production in peripheral nerves of mice fed a ketogenic diet.

What is the central question of this study? Do peripheral sensory neurons metabolize fat-based fuel sources, and does a ketogenic diet modify these processes? What is the main finding and its importance We show that peripheral axons from mice fed a ketogenic diet respond to fat-based fuel sources with reduced respiration and H2 O2 emission compared with mice fed a control diet. These results add to our understanding of the responses of sensory neurons to neuropathy associated with poor diet, obesity and metabolic syndrome. These findings should be incorporated into current ideas of axonal protection and might identify how dietary interventions may change mitochondrial function in settings of sensory dysfunction. Metabolic syndrome and obesity are increasing epidemics that significantly impact the peripheral nervous system and lead to negative changes in sensation and peripheral nerve function. Research to understand the consequences of diet, obesity and fuel usage in sensory neurons has commonly focused on glucose metabolism. Here, we tested whether mouse sensory neurons and nerves have the capacity to metabolize fat-based fuels (palmitoyl-CoA) and whether these effects are altered by feeding of a ketogenic (90%kcal fat) diet compared with a control diet (14%kcal fat). Male C57Bl/6 mice were placed on the diets for 10weeks, and after the mice were killed, the dorsal root ganglion (DRG) and sciatic nerve (SN) were placed in an Oroboros oxygraph-2K to examine diet-induced alterations in metabolism (respiration) of palmitoyl-CoA and H2 O2 emission (fluorescence). In addition, RNAseq was performed on the DRG of mice fed a control or a ketogenic diet for 12weeks, and genes associated with mitochondrial respiratory function were analysed. Our results suggest that the sciatic nerves from mice fed a ketogenic diet display reduced O2 respiration and H2 O2 emission when metabolizing palmitoyl-CoA compared with mice fed a control diet. Assessments of changes in mRNA gene expression reveal alterations in genes encoding the NADH dehydrogenase complex and complexIV, which could alter production of reactive oxygen species. These new findings highlight the ability of sensory neurons and axons to oxidize fat-based fuel sources and show that these mechanisms are adaptable to dietary changes.

26: Severe placental insufficiency, acidemia and imminent stillbirth are associated with changes in circulating levels of mRNA coding NR4A2, RCBTB2 and EMP1

To identify mRNA in the maternal circulation associated with severe preterm fetal growth restriction (FGR), fetal acidemia and imminent stillbirth. We performed a prospective study across six referral hospitals. We obtained maternal blood from 128 cases of FGR delivered by cesarean section <34 weeks due to fetal compromise, and 84 healthy gestation matched controls. FGR samples were collected within 2 hours prior to birth and umbilical cord pH was measured to determine fetal acidemia status. We performed RNA-seq on all 212 samples and bioinformatics (linear model, switch box and PLSDA) to identify genes differentially expressed in the FGR group. We used PCR to validate top genes (ie those consistently deranged in cases compared to controls, identified by bioinformatics), and also to examine those genes differentially expressed with fetal acidemia. We then measured the top genes in a separate cohort of six women whose pregnancies were affected by preterm FGR and ended in stillbirth. The baseline clinical characteristics of the FGR and control cohort are shown on the table. There were global changes in mRNA gene expression (11,402 genes differentially expressed with adjusted p<0.05) in the maternal circulation among the FGR cohort (n=128) vs gestationally matched controls (n=84). Using bioinformatics on the RNA-Seq data followed by PCR validation, we identified 8 genes that were differentially expressed with FGR with a very high level of significance. Of those, NR4A2 (Fig. A,B) and RCBTB2 were also differentially expressed when the FGR cohort was split according to whether umbilical cord pH at delivery was ≤7.2 (low pH, acidemic fetus) or >7.2. Notably, of these 8 genes that were differentially expressed with FGR, mRNA coding NR4A2 (Fig. C), RCBTB2 and EMP1 were consistently deranged in the circulation of six women with imminent stillbirth (last blood before demise, gestational age range 19-28 weeks) compared to 24 gestational age-matched controls (ongoing pregnancies). Severe preterm fetal growth restriction, in utero acidemia and imminent stillbirth are associated with differential expression of mRNA coding NR4A2, RCBTB2 and EMP1 in maternal blood. They have potential as markers of severe placental insufficiency and the ‘at risk’ fetus.View Large Image Figure ViewerDownload Hi-res image Download (PPT)

Neurobehavioural effects of Lactobacillus rhamnosus GG alone and in combination with prebiotics polydextrose and galactooligosaccharide in male rats exposed to early-life stress

Early life is a period of significant brain development when the brain is at its most plastic and vulnerable. Stressful episodes during this window of development have long-lasting effects on the central nervous system. Rodent maternal separation (MS) is a reliable model of early-life stress and induces alterations in both physiology and behaviour. Intriguingly, the gut microbiota of MS offspring differ from that of non-separated offspring, suggesting a mechanistic role for the microbiota–gut–brain axis. Hence, we tested whether dietary factors known to affect the gut microbiota alter the neurobehavioural effects of MS. The impact of consuming diet containing prebiotics polydextrose (PDX) and galactooligosaccharide (GOS) alone or in combination with live bacteria Lactobacillus rhamnosus GG (LGG) from weaning onwards in rats subjected to early-life MS was assessed. Adult offspring were assessed for anxiety-like behaviour in the open field test, spatial memory using the Morris water maze, and reactivity to restraint stress. Brains were examined via PCR for changes in mRNA gene expression. Here, we demonstrate that diets containing a combination of PDX/GOS and LGG attenuates the effects of early-life MS on anxiety-like behaviour and hippocampal-dependent learning with changes to hippocampal mRNA expression of genes related to stress circuitry, anxiety and learning.

Chronic stress induces persistent changes in global DNA methylation and gene expression in the medial prefrontal cortex, orbitofrontal cortex, and hippocampus

Chronic stress is associated with a plethora of cognitive symptoms such as emotional dysregulation and impaired executive function that have been attributed to modifications in neuroanatomy in the orbitofrontal cortex (OFC), medial prefrontal cortex (mPFC), and hippocampus (HPC). While many studies have examined stress-induced changes in neuronal morphology, synaptic plasticity, and cellular function, there has been little investigation into persistent changes in gene expression that may be responsible for the maintenance of these changes. This study exposed adult rats to a chronic stressor and then examined changes in mRNA gene expression in the OFC, mPFC and HPC following a two-week withdrawal period. mRNA bio-sequencing results revealed sex- and region-dependent changes. Surprisingly the greatest changes in gene expression were found in the OFC, and similar to anatomical studies, analysis of gene changes with Ingenuity Pathway Analysis software demonstrated that the mPFC and OFC exhibited contrasting activation of canonical pathways and functional networks. The HPC demonstrated the largest degree of sex-dependent change in gene expression. In general, chronic stress induced persistent changes in gene expression in the three brain regions we examined and these changes could be associated with the commonly reported cognitive symptoms. The current study highlights the region- and sex-dependent nature of the brain’s response to chronic stress and the difficulty we face when attempting to develop treatment options.

Dietary modulation of the expression of genes involved in short-chain fatty acid absorption in the rumen epithelium is related to short-chain fatty acid concentration and pH in the rumen of goats

We have tested the hypothesis that increased concentrate intake induces mRNA abundance alterations of genes involved in short-chain fatty acid (SCFA) absorption in the rumen epithelium of goats and these changes of mRNA abundance are probably related to ruminal SCFA concentration and ruminal pH. Goats (n=12) were randomly allocated to 2 groups and fed either a low-concentrate (LC) diet (10% concentrate; n=6) or a medium-concentrate (MC) diet (35% concentrate; n=6) in 2 equal portions daily. Goats were fed separately with their respective diet for 3 wk. The goats were slaughtered 6h after the morning feeding on d 22. In vivo, goats in the MC treatment exhibited a greater ruminal SCFA concentration (81.9mM) compared with those in the LC treatment (58.0mM), and the pH decreased from 7.03 to 6.63. Correspondingly, mRNA expression of candidates for SCFA−/HCO3− exchangers, namely downregulated in adenoma (DRA), putative anion transporter 1 (PAT1), and anion exchanger 2 (AE2) were increased in the MC group. Further, upregulation in monocarboxylate transporter 1 (MCT1) and monocarboxylate transporter 4 (MCT4) mRNA abundances was observed in the MC group. The expression of genes that help the rumen epithelial cells to maintain intracellular pH, including Na+/H+ exchanger 1 (NHE1), NHE2, NHE3, vacuolar H+ ATPase subunit B (vH+ATPase), and Na+/K+ ATPase pump subunit α1 (Na+/K+ATPase) were also enhanced in the MC group relative to the LC group. During in vitro studies with isolated rumen epithelial cells from goats, exposure to a pH of 6.8 increased MCT1 mRNA expression after 24h of culture, whereas the mRNA expression of AE2 was downregulated. The presence of SCFA (20mM) in the medium increased DRA, PAT1, AE2, MCT1, and Na+/K+ATPase mRNA expression. The expression of vH+ATPase was decreased by increased SCFA concentration. The mRNA expression of MCT4 did not vary in vitro with pH (6.8) or SCFA (20mM). The expression of DRA was increased by synergistic effects of higher SCFA concentration and lower pH, similar to that of MCT1. Thus, diet-dependent rumen epithelial mRNA expression changes in genes involved in SCFA absorption are probably related to ruminal SCFA concentration and pH.

Effect of CD200 and CD200R1 expression within tissue grafts on increased graft survival in allogeneic recipients

In transgenic mice over-expressing CD200 (CD200tg) graft survival is associated with increased intra-graft expression of mRNAs for genes associated with altered T cell subset differentiation (Foxp3; TGFβ; IL-10). Grafts are rejected in recipients lacking the inhibitory receptor for CD200, CD200R1.We compared grafts of C57BL/6 skin taken from control, CD200KO, CD200tg, CD200R1KO or CD200tg.CD200R1KO C57BL/6 donor mice transplanted to control or CD200tg BALB/c recipients. Animals received either low-dose rapamycin (0.5mg/kg), which only enhanced survival in CD200tg mice, or high dose rapamycin (1.5mg/kg) which increased graft survival in all recipients. Recipient draining lymph nodes (DLNs) were analyzed at 14days post grafting in mixed leukocyte cultures (MLCs) with irradiated BL/6 or C3H/HeJ stimulator cells, assaying antigen-specific CTL at day 5. MLC responses were correlated with changes in mRNA gene expression in skin tissue harvested from the same recipients, focusing on genes altered in “graft-accepting” CD200tg recipients. Tissue histology was used to assess graft infiltrating Foxp3+ Tregs, mast cells (MCs) and their degranulation.CD200tg grafts were accepted in control but not CD200KO/CD200R1KO recipients, along with decreased degranulation in graft MCs, diminished DLN MLC responses, and augmented intragraft Foxp3, TGFβ, IL-10 and mast cell gene expression. Skin grafts from either CD200KO or CD200R1KO donors to control mice were rejected, with no change in DLN MLC responses, no altered graft gene expression from that seen using control skin grafts, and pronounced graft MC degranulation. Our data highlight a role for both graft and host CD200/CD200R expression in increased allograft survival.

Early gene expression changes with rush immunotherapy

BackgroundTo examine whether whole genome expression profiling could reveal changes in mRNA expression of peripheral blood mononuclear cells (PBMC) from allergic patients undergoing rush immunotherapy (RIT) that might be manifest within the first few months of treatment.MethodsFor this study, PBMC from three allergic patients undergoing RIT were assessed at four timepoints: prior to RIT, at 1 week and 7 week post-RIT, during build-up and at 4 months, after establishment of a maintenance dose. PBMC mRNA gene expression changes over time were determined by oligonucleotide microarrays using the Illumina Human-6 BeadChip Platform, which simultaneously interrogates expression profiles of > 47,000 transcripts. Differentially expressed genes were identified using well-established statistical analysis for microarrays. In addition, we analyzed peripheral blood basophil high-affinity IgE receptor (Fc epsilon RI) expression and T-regulatory cell frequency as detected by expression of CD3+CD4+CD25bright cells at each timepoint using flow cytometry.ResultsIn comparing the initial 2 timepoints with the final 2 timepoints and analyzing for genes with ≥1.5-fold expression change (p less than or equal to 0.05, BH-FDR), we identified 507 transcripts. At a 2-fold change (p less than or equal to 0.05, BH-FDR), we found 44 transcripts. Of these, 28 were up-regulated and 16 were down-regulated genes. From these datasets, we have identified changes in immunologically relevant genes from both the innate and adaptive response with upregulation of expressed genes for molecules including IL-1β, IL-8, CD40L, BTK and BCL6. At the 4 month timepoint, we noted a downward trend in Fc epsilon RI expression in each of the three patients and increased allergen-specific IgG4 levels. No change was seen in the frequency of peripheral T-regulatory cells expressed over the four timepoints.ConclusionsWe observed significant changes in gene expression early in peripheral blood samples from allergic patients undergoing RIT. Moreover, serum levels for allergen specific IgG4 also increased over the course of treatment. These studies suggest that RIT induces rapid and dynamic alterations in both innate and adaptive immunity which can be observed in the periphery of allergic patients. These alterations could be directly related to the therapeutic shift in the allergen-specific class of immunoglobulin.

PGC‐1α encoded by the PPARGC1A gene regulates oxidative energy metabolism in equine skeletal muscle during exercise

Peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) has emerged as a critical control factor in skeletal muscle adaptation to exercise, acting via transcriptional control of genes responsible for angiogenesis, fatty acid oxidation, oxidative phosphorylation, mitochondrial biogenesis and muscle fibre type composition. In a previous study, we demonstrated a significant increase in mRNA expression for the gene encoding PGC-1α (PPARGC1A) in Thoroughbred horse skeletal muscle following a single bout of endurance exercise. In this study, we investigated mRNA expression changes in genes encoding transcriptional coactivators of PGC-1α and genes that function upstream and downstream of PGC-1α in known canonical pathways. We used linear regression to determine the associations between PPARGC1A mRNA expression and expression of the selected panel of genes. Biopsy samples were obtained from the gluteus medius pre-exercise (T(0) ), immediately post-exercise (T(1) ) and 4 h post-exercise (T(2) ). Significant (P < 0.05) expression fold change differences relative to T(0) were detected for genes functioning in angiogenesis (ANGP2 and VEGFA); Ca(2+) -dependent signalling pathway (PPP3CA); carbohydrate/glucose metabolism (PDK4); fatty acid metabolism/mitochondrial biogenesis (PPPARGC1B); haem biosynthetic process (ALAS1); insulin signalling (FOXO1, PPPARGC1A and SLC2A4); mitogen-activated protein kinase signalling (MAPK14 and MEF2A); and myogenesis (HDAC9). Gene expression associations were identified between PPARGC1A and genes involved in angiogenesis, mitochondrial respiration, glucose transport, insulin signalling and transcriptional regulation. These results suggest that PGC-1α and genes regulated by PGC-1α play significant roles in the skeletal muscle response to exercise and therefore may contribute to performance potential in Thoroughbred horses.

Analysis of messenger RNA expression by in situ hybridization using RNA probes synthesized via in vitro transcription

The analysis of the spatial patterning of mRNA expression is critically important for assigning functional and physiological significance to a given gene product. Given the tens of thousands of mRNAs in the mammalian genome, a full assessment of individual gene functions would ideally be overlaid upon knowledge of the specific cell types expressing each mRNA. In situ hybridization approaches represent a molecular biological/histological method that can reveal cellular patterns of mRNA expression. Here, we present detailed procedures for the detection of specific mRNAs using radioactive RNA probes in tissue sections followed by autoradiographic detection. These methods allow for the specific and sensitive detection of spatial patterns of mRNA expression, thereby linking mRNA expression with cell type and function. Radioactive detection methods also facilitate semi-quantitative analyses of changes in mRNA gene expression.

Identification of potential gene expression biomarkers for the surveillance of anabolic agents in bovine blood cells

In the EU, the use of anabolic steroids in food producing animals has been forbidden since 1988. The routine methods used in practice are based on the detection of hormonal residues. To overcome these routine methods, growth-promoting agents are sometimes administered at concentrations below the detection limit and new anabolic substances are designed. Therefore, new monitoring systems are needed to overcome the misuse of anabolic agents in meat production. In this study, a new monitoring system was applied: the quantification of mRNA gene expression changes by quantitative real time reverse transcription polymerase chain reaction (qRT-PCR). Blood was selected as ideal tissue for biomarker screening. From the literature, it is known that steroid hormones affect mRNA gene expression of the different blood cells, which can easily be taken from the living animal. In an animal trial, 18 Nguni heifers were separated to two groups of nine animals. One group served as untreated control and the other group was treated with a combination of trenbolone acetate plus estradiol for 39 days in order to allow the detection of the effect on mRNA expression in blood at three time points. Candidate genes used for developing a biomarker pattern were chosen by screening the actual literature for anabolic effects on blood cells. It could be demonstrated that the combination of trenbolone acetate plus estradiol significantly influences mRNA expression of the steroid receptors (ER-α and GR-α), the apotosis regulator Fas, the proinflammatory interleukins IL-1α, IL-1β and IL-6 and of MHCII, CK, MTPN, RBM5 and Actin-β. Advanced statistical analysis by Principal Components Analysis (PCA) indicated that these genes represent potential biomarkers for this hormone combination in whole blood.

The Influence of Eccentric and Concentric Exercise on Skeletal Muscle Regulators in Young Women

PURPOSE: To evaluate changes in myostatin, follistatin and MyoD mRNA gene expression using concentric exercise (CE) and eccentric exercise (EE) as a stimulus to better understand the mechanisms of muscle hypertrophy in young women. METHODS: Single-leg maximal eccentric or concentric isokinetic exercise was performed using the Cybex NormTM dynamometer (Cybex International Inc. Ronkonkoma, New York) at 60° /s. Ten sets of ten repetitions with 20 second rest between sets were completed by each subject. Three muscle biopsies of the vastus lateralis were obtained from the exercised leg at baseline (1st biopsy), 8 hours after the first exercise bout (2nd biopsy), and 8 hours after the seventh and final exercise bout performed 2 weeks after the first exercise session (3rd biopsy). mRNA gene expression was analyzed using RT-PCR methods. 18s ribosomal RNA was used as the internal standard to determine relative expression of mRNAs for myostatin, follistatin, and MyoD. Paired t-tests were used to compare changes in mRNA gene expression within groups (Eccentric or Concentric). Independent t-tests were performed to test group differences (Eccentric versus Concentric). A probability level of P ≤ 0.05 was used to determine statistical significance with Bonferroni adjustments. RESULTS: There were no significant fold changes in the CE group for myostatin, follistatin, and MyoD mRNA gene expression between the first and second biopsies as well as the first and third biopsies (P>0.17). Similarly, there were no significant changes in the EE group for the same variables (P>0.11). In addition, there were no significant differences between the EE and CE groups (P≥0.05). CONCLUSIONS: Our data suggests that a single bout or multiple bouts (7) of maximal eccentric or concentric exercise does not significantly alter myostatin, follistatin, or MyoD mRNA gene expression in young women. Therefore, the type of exercise stimulus does not appear to differentially alter mRNA gene expression of hypertrophic myogenic regulators.

Changes in mRNA gene expression during growth in the femoral head of the young rat

The rate of physeal growth slows as an animal matures with changes in mRNA gene expression due to the altered cellular activity. To measure the change in gene expression during the juvenile growth period, the femoral head, enclosing the proximal femoral physis, primary spongiosa, and articular cartilage, was collected from both femora of 16 female Sprague–Dawley rats between 4 and 10 weeks of age. One femur of each rat had had a mid-diaphyseal femoral fracture at 4 weeks of age. RNA was extracted and hybridized to 16 Affymetrix Rat Genomic 230 2.0 GeneChip microarrays with probe sets for 31,000 genes of which 18,200 were expressed. Of these, 8002 genes had a significant change in gene expression during growth, about half increasing and half decreasing. These changes included up-regulation with time of genes related to cartilage, blood vessels, osteoprotegerin, osteomodulin, and most ribosomal proteins. There was down-regulation with maturity of genes related to bone, growth-promoting cytokines, G proteins, GTPase-mediated signal transduction factors, cytokine receptors, mitosis, integrin-linked kinase, and the cytoskeleton. In summary, the slowing of growth with maturity was associated with changes in mRNA gene expression in the femoral head for a large number of genes. These changes in gene expression between young and mature rats suggest factors which are important for the support of the rapid linear growth during early life.

Gene expression clustering using self-organizing maps: analysis of the macrophage response to particulate biomaterials

The most common cause of total joint replacement failure is peri-implant bone loss causing pain and prosthesis loosening. This process, known as osteolysis or aseptic loosening, is characterized by macrophage phagocytosis of particulate implant wear debris. In an incompletely defined step, particulate biomaterial debris induces macrophages to release a variety of inflammatory mediators and signaling proteins that lead to bone loss. In an in vitro model of this process, we used microarray technology and data analysis techniques, including the use of self-organizing maps (SOMs), to understand the mRNA gene expression changes occurring in macrophages exposed to clinically relevant particles of ultra-high molecular weight polyethylene and TiAlV alloy. Earlier studies have been limited by technology that only allowed analysis of a few genes at a time, but the microarray techniques used in this paper generate the quantitative analysis of over a thousand genes simultaneously. Our microarray analysis utilized an SOM clustering to elucidate general patterns in the data, lists of top up- and down-regulated genes for each time point and genes with differential expression under different biomaterial exposures. The expression levels of the majority of genes ( > 95 % ) did not vary over time or with exposure to different biomaterials, but a few important genes, such as TNF- α , IL- 1 β , IL-6, and MIP 1 α , proved to be highly regulated in response to biomaterial exposure. We also uncovered a novel set of genes, which not only validates and logically extends the current model of the pathogenesis of osteolysis and aseptic loosening, but also provides new targets for further research and therapeutics.