Differential mRNA Expression Profiles Research Articles

Altered Peripheral Blood Gene Expression in Childhood Cancer Survivors With Anthracycline-Induced Cardiomyopathy - A COG-ALTE03N1 Report.

Background Anthracycline-induced cardiomyopathy is a leading cause of premature death in childhood cancer survivors, presenting a need to understand the underlying pathogenesis. We sought to examine differential blood-based mRNA expression profiles in anthracycline-exposed childhood cancer survivors with and without cardiomyopathy. Methods and Results We designed a matched case-control study (Children's Oncology Group-ALTE03N1) with mRNA sequencing on total RNA from peripheral blood in 40 anthracycline-exposed survivors with cardiomyopathy (cases) and 64 matched survivors without (controls). DESeq2 identified differentially expressed genes. Ingenuity Pathway Analyses (IPA) and Gene Set Enrichment Analyses determined the potential roles of altered genes in biological pathways. Functional validation was performed by gene knockout in human-induced pluripotent stem cell-derived cardiomyocytes using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) technology. Median age at primary cancer diagnosis for cases and controls was 8.2 and 9.7 years, respectively. Thirty-six differentially expressed genes with fold change ≥±2 were identified; 35 were upregulated. IPA identified "hepatic fibrosis" and "iron homeostasis" pathways to be significantly modulated by differentially expressed genes, including toxicology functions of myocardial infarction, cardiac damage, and cardiac dilation. Leading edge analysis from Gene Set Enrichment Analyses identified lactate dehydrogenase A (LDHA) and cluster of differentiation 36 (CD36) genes to be significantly upregulated in cases. Interleukin 1 receptor type 1, 2 (IL1R1, IL1R2), and matrix metalloproteinase 8, 9 (MMP8, MMP9) appeared in multiple canonical pathways. LDHA-knockout human-induced pluripotent stem cell-derived cardiomyocytes showed increased sensitivity to doxorubicin. Conclusions We identified differential mRNA expression profiles in peripheral blood of anthracycline-exposed childhood cancer survivors with and without cardiomyopathy. Upregulation of LDHA and CD36 genes suggests metabolic perturbations in a failing heart. Dysregulation of proinflammatory cytokine receptors IL1R1 and IL1R2 and matrix metalloproteinases, MMP8 and MMP9 indicates structural remodeling that accompanies the clinical manifestation of symptomatic cardiotoxicity.

Exploratory Transcriptomic Profiling Reveals the Role of Gut Microbiota in Vascular Dementia.

Stroke is the second most common cause of cognitive impairment and dementia. Vascular dementia (VaD), a cognitive impairment following a stroke, is common and significantly impacts the quality of life. We recently demonstrated via gut microbe transplant studies that the gut microbe-dependent trimethylamine-N-oxide (TMAO) pathway impacts stroke severity, both infarct size and long-term cognitive outcomes. However, the molecular mechanisms that underly the role of the microbiome in VaD have not been explored in depth. To address this issue, we performed a comprehensive RNA-sequencing analysis to identify differentially expressed (DE) genes in the ischemic cerebral cortex of mouse brains at pre-stroke and post-stroke day 1 and day 3. A total of 4016, 3752 and 7861 DE genes were identified at pre-stroke and post-stroke day 1 and day 3, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated pathways of neurodegeneration in multiple diseases, chemokine signaling, calcium signaling, and IL-17 signaling as the key enriched pathways. Inflammatory response genes interleukin-1 beta (Il-1β), chemokines (C-X-C motif chemokine ligand 10 (Cxcl10), chemokine ligand 2 (Ccl2)), and immune system genes (S100 calcium binding protein 8 (S100a8), lipocalin-2 (Lcn2)) were among the most significantly upregulated genes. Hypocretin neuropeptide precursor (Hcrt), a neuropeptide, and transcription factors such as neuronal PAS domain protein 4 (Npas4), GATA binding protein 3 (Gata3), and paired box 7 (Pax7) were among the most significantly downregulated genes. In conclusion, our results indicate that higher plasma TMAO levels induce differential mRNA expression profiles in the ischemic brain tissue in our pre-clinical stroke model, and the predicted pathways provide the molecular basis for regulating the TMAO-enhanced neuroinflammatory response in the brain.

Potential New Therapeutic Approaches for Cisplatin-Resistant Testicular Germ Cell Tumors.

Testicular germ cell tumors (TGCTs), a group of heterogeneous neoplasms, are the most frequent tumors of teenagers and young men, with the incidence rising worldwide. High cure rates can be achieved through cisplatin (CDDP)-based treatment, but approximately 10% of patients present refractory disease and virtually no treatment alternatives. Here, we explored new strategies to treat CDDP-resistant. In vitro TGCT CDDP-resistance model was established and differential mRNA expression profiles were evaluated using NanoString technology. Then, TGCT cell lines were treated with four potential drugs (PCNA-I1, ML323, T2AA, and MG-132) to overcome CDDP-resistance. We found several differentially expressed genes related to DNA repair and cell cycle regulation on CDDP-resistant cell line (NTERA-2R) compared to parental cell line (NTERA-2P), and the proteasome inhibitor MG-132 demonstrated cytotoxic activity in all cell lines evaluated, even at a nanomolar range. MG-132 also enhanced cell lines' sensitivity to CDDP, increasing apoptosis in both NTERA-2P and NTERA-2R. MG-132 emerges as a potential new drug to treat CDDP-resistant TGCT. Targeted therapy based on molecular mechanism insights may contribute to overcome acquired chemotherapy CDDP-resistance.

Transcriptome analysis revealed gene expression feminization of testis after exogenous tetrodotoxin administration in pufferfish Takifugu flavidus

Tetrodotoxin (TTX) is a deadly neurotoxin and usually accumulates in large amounts in the ovaries but is non-toxic or low toxic in the testis of pufferfish. The molecular mechanism underlying sexual dimorphism accumulation of TTX in ovary and testis, and the relationship between TTX accumulation with sex related genes expression remain largely unknown. The present study investigated the effects of exogenous TTX treatment on Takifugu flavidus. The results demonstrated that exogenous TTX administration significantly incresed level of TTX concentration in kidney, cholecyst, skin, liver, heart, muscle, ovary and testis of the treatment group (TG) than that of the control group (CG). Transcriptome sequencing and analysis were performed to study differential expression profiles of mRNA and piRNA after TTX administration of the ovary and testis. The results showed that compared with female control group (FCG) and male control group (MCG), TTX administration resulted in 80 and 23 piRNAs, 126 and 223 genes up and down regulated expression in female TTX-treated group (FTG), meanwhile, 286 and 223 piRNAs, 2 and 443 genes up and down regulated expression in male TTX-treated group (MTG). The female dominant genes cyp19a1, gdf9 and foxl2 were found to be up-regulated in MTG. The cyp19a1, whose corresponding target piRNA uniq_554482 was identified as down-regulated in the MTG, indicating the gene expression feminization in testis after exogenous TTX administration. The KEGG enrichment analysis revealed that differentially expressed genes (DEGs) and piRNAs (DEpiRNAs) in MTG vs MCG group were more enriched in metabolism pathways, indicating that the testis produced more metabolic pathways in response to exogenous TTX, which might be a reason for the sexual dimorphism of TTX distribution in gonads. In addition, TdT-mediated dUTP-biotin nick end labeling staining showed that significant apoptosis was detected in the MTG testis, and the role of the cell apoptotic pathways was further confirmed. Overall, our research revealed that the response of the ovary and testis to TTX administration was largely different, the ovary is more tolerant whereas the testis is more sensitive to TTX. These data will deepen our understanding on the accumulation of TTX sexual dimorphism in Takifugu.

Aberrant messenger RNA expression in peripheral blood mononuclear cells is associated with gouty arthritis.

Gouty arthritis (GA) is a type of self-limiting inflammatory arthritis caused by deposition of monosodium urate (MSU). This study aimed to analyze the expression variation of messenger RNAs (mRNAs) in GA patients and investigated the role of mRNAs in GA pathogenesis. Five patients with acute GA (AGA), 5 with non-acute GA (NAGA), and 5 healthy controls (HC) were recruited to examine differential mRNA expression profiles in peripheral blood mononuclear cells (PBMCs) and explore whether mRNA is involved in the pathogenesis of AGA. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to study the biological functions of differentially expressed mRNA and the relationship between genes and signal pathways. Compared with HC, the AGA group had 1456 differentially expressed mRNAs, while the NAGA group had 437 differentially expressed mRNAs and compared with the NAGA group, 115 differentially expressed mRNAs were found in the AGA group. GO analysis showed that the differentially expressed mRNA in the AGA group was mainly enriched in processes related to leukocyte activation and immune response, while KEGG analysis showed that "Staphylococcus aureus infection" and "Cytokine-cytokine receptor interaction" are enriched in the up-regulated mRNAs in the AGA group. This study identified genes and pathways that are differentially expressed during the onset of AGA, which might reveal part of the pathogenesis of the disease and provide clues to explaining the severe pain associated with disease onset and the rapid development of inflammatory response that subsides by itself.

Differential Expression Profiles of mRNA and Noncoding RNA and Analysis of Competitive Endogenous RNA Regulatory Networks in Nonalcoholic Steatohepatitis.

Nonalcoholic steatohepatitis (NASH) is a liver disease caused by multiple factors, and there is no approved pharmacotherapy. The pathogenesis of NASH remains underexplored. In this study, differentially expressed circular RNAs (circRNAs) were obtained by analyzing NASH-related circRNA datasets, and then, corresponding target microRNAs (miRNAs) and messenger RNAs (mRNAs) were predicted to construct a circRNA–miRNA–mRNA regulatory network. On this basis, a total of 38 circRNAs, 7 miRNAs, and 10 mRNAs were screened out. The present study reveals novel circRNA biomarkers of NASH and reports a potential competing endogenous RNA (ceRNA) regulatory network that might provide insights for further investigation into the underlying pathogenesis of NASH.

High-Throughput Sequencing Reveals CXCR4 and IGF1 Behave Different Roles in Weightlessness Osteoporosis.

Objective This study is aimed at screening the differential expression profiles of mRNA under weightlessness osteoporosis through high-throughput sequencing technology, as well as investigating the pathogenesis of weightlessness osteoporosis at the molecular level especially in bone marrow mesenchymal stem cells (BMSCs). Methods The mouse bone marrow mesenchymal stem cell line was divided into ground group and simulated microgravity (SMG) group. BMP-2 was used to induce osteogenic differentiation, and SMG group was placed into 2D-gyroscope to simulate weightless condition. Transcriptome sequencing was performed by Illumina technology, DEGs between ground and SMG group was conducted using the DEseq2 algorithm. Molecular functions and signaling pathways enriched by DEGs were then comprehensively analyzed via multiple bioinformatic approaches including but not limited to GO, KEGG, GSEA, and PPI analysis. Results A total of 263 DEGs were identified by comparing these 2 groups, including 186 upregulated genes and 77 downregulated genes. GO analysis showed that DEGs were enriched in osteoblasts, osteoclasts cell proliferation, differentiation, and apoptosis; KEGG analysis revealed that DEGs were significantly enriched in the TNF signaling pathway and FoxO signaling pathway; the enrichment results from Reactome database displayed that DEGs were mainly involved in the transcription of Hoxb3 gene, RUNX1 recruitment KMT2A gene, and activation of Hoxa2 chromatin signaling pathway. The four genes, IL6, CXCR4, IGF1, and PLOD2, were identified as hub genes for subsequent analysis. Conclusions This study elucidated the significance of 10 hub genes in the development of weightlessness osteoporosis. In addition, the results of this study provide a theoretical basis and novel ideas for the subsequent research of the pathogenesis and clinical treatment of weightlessness osteoporosis.

Impact of selenium on cerebellar injury and mRNA expression in offspring of rat exposed to methylmercury

During the fetal development stage, the Central Nervous System (CNS) is particularly sensitive to methylmercury (MeHg). However, the mechanism underlying the antagonistic effect of selenium (Se) on MeHg toxicity is still not fully understood. In this study, female rat models with MeHg and Se co-exposure were developed. Pathological changes in the cerebellum and differential mRNA expression profiles in offspring rats were studied. In the MeHg-exposed group, a large number of Purkinje cells showed pathological changes and mitochondria were significantly swollen; co-exposure with Se significantly improved the structure and organization of the cerebellum. In total, 378 differentially expressed genes (DEGs) (including 284 up-regulated genes and 94 down-regulated genes) in the cerebellum of the MeHg-exposed group and 210 DEGs (including 84 up-regulated genes and 126 down-regulated genes) in the cerebellum of the MeHg+Se co-exposed group were identified. The genes involved in neurotransmitter synthesis and release and calcium ion balance in the cerebellum were significantly up-regulated in the MeHg-exposed group. These genes in the MeHg+Se co-exposed group were not changed or down-regulated. These findings demonstrate that the neurotoxicity caused by MeHg exposure is related to the up-regulation of multiple genes in the nerve signal transduction and calcium ion signal pathways, which are closely related to impairments in cell apoptosis and learning and memory. Supplementation with Se can mitigate the changes to related genes and protect neurons in the mammalian brain (especially the developing cerebellum) from MeHg toxicity. Se provides a potential intervention strategy for MeHg toxicity.

Immune-Related Genes: Potential Regulators and Drug Therapeutic Targets in Hypertrophic Cardiomyopathy

Background. Accumulating evidence shows that the innate immune system is a key player in cardiovascular repair and regeneration, but little is known about the role of immune-related genes (IRGs) in hypertrophic cardiomyopathy (HCM). Methods. The differential mRNA expression profiles of HCM samples were downloaded from the Gene Expression Omnibus (GEO) dataset (GSE89714), and the IRG expression profile was obtained from the ImmPort database. The regulatory pathways of IRGs in HCM were screened out through discrepantly expressive genes (DEGs) analysis, enrichment of gene function/pathway analysis, and protein-protein interaction (PPI) network. Besides, hub IRGs in the PPI network were selected for drug prediction. Results. A total of 854 genes were differentially expressed in HCM, of which 88 were IRGs. Functional enrichment analysis revealed that 88 IRGs were mainly involved in the biological processes (BP) of SMAD protein pathway, smooth muscle cell proliferation, protein serine/threonine kinase, and mitogen-activated protein kinase (MAPK) cascade. Cytokine-cytokine receptor interaction, TGFβ signaling pathway, PI3K-Akt signaling pathway, and MAPK signaling pathway were enriched in the pathway enrichment analysis of these 88 IRGs. Furthermore, the PPI regulatory network of IRGs was constructed, and 10 hub IRGs were screened out to construct a regulatory network for HCM. 4 transcription factors (TFs) were the major regulator of 10 hub IRGs. Finally, these 10 hub IRGs were entered into the pharmacogenomics database for prediction, and the relevant drugs were obtained. Conclusions. In this study, 10 hub IRGs were coexpressed with 4 TFs to construct a regulatory network for HCM. Drug prediction of these 10 hub IRGs proposed potential therapeutic agents that could be used in HCM. These results indicate that IRGs are potential regulators and drug therapeutic targets in HCM.

BRD2 induces drug resistance through activation of the RasGRP1/Ras/ERK signaling pathway in adult T-cell lymphoblastic lymphoma.

BackgroundAdult patients with T‐cell lymphoblastic lymphoma (T‐LBL) are treated with high‐intensity chemotherapy regimens, but the response rate is still unsatisfactory because of frequent drug resistance. We aimed to investigate the potential mechanisms of drug resistance in adults with T‐LBL.MethodsGene expression microarray was used to identify differential mRNA expression profiles between chemotherapy‐resistant and chemotherapy‐sensitive adult T‐LBL tissues. Real‐time PCR and immunohistochemistry were performed to detect the expression of bromodomain‐containing protein 2 (BRD2) and c‐Myc in fresh‐frozen T‐LBL tissues from 85 adult patients. The Ras pull‐down assay was performed to monitor Ras activation. Chromatin immunoprecipitation assays were used to analyze the binding of E2F transcription factor 1 (E2F1)/BRD2 to the RAS guanyl releasing protein 1 (RasGRP1) promoter region. The drug resistance effect and mechanism of BRD2 were determined by both in vivo and in vitro studies.ResultsA total of 86 chemotherapy resistance‐related genes in adult T‐LBL were identified by gene expression microarray. Among them, BRD2 was upregulated in chemotherapy‐resistant adult T‐LBL tissues and associated with worse progression‐free survival and overall survival of 85 adult T‐LBL patients. Furthermore, BRD2 suppressed doxorubicin (Dox)‐induced cell apoptosis both in vitro and in vivo. The activation of RasGRP1/Ras/ERK signaling might contribute to the Dox resistance effect of BRD2. Besides, OTX015, a bromodomain and extra‐terminal (BET) inhibitor, reversed the Dox resistance effect of BRD2. Patient‐derived tumor xenograft demonstrated that the sequential use of OTX015 after Dox showed superior therapeutic effects.ConclusionsOur data showed that BRD2 promotes drug resistance in adult T‐LBL through the RasGRP1/Ras/ERK signaling pathway. Targeting BRD2 may be a novel strategy to improve the therapeutic efficacy and prolong survival of adults with T‐LBL.

SU2 - CORRELATION ANALYSIS OF miRNA AND mRNA EXPRESSION PROFILES IN PERIPHERAL BLOOD MONONUCLEAR CELLS FROM ADHD PATIENTS AND CONTROLS

Background Attention Deficit Hyperactivity Disorders (ADHD) is a neurodevelopmental disorder characterized by impairment in sustaining attention and inability to control impulses and modulate activity level. The aetiology of ADHD is complex, involving genetic and environmental factors, with an estimated heritability of 70–80%. Nevertheless, inconsistencies in the results of the genetic studies on ADHD may be explained, in part, by epigenetic mechanisms such as microRNAs (miRNAs) which play important roles in the control of gene expression by pairing to target mRNAs. Under the hypothesis that alterations in the processing or target binding of miRNAs may result in differential mRNA expression profiles predisposing to ADHD, we performed mRNA and miRNA expression profiling in Peripheral Blood Mononuclear Cells (PBMCs) of 103 persistent ADHD individuals and 115 controls. Methods miRNA and mRNA expression profiling in PBMCs of 103 ADHD patients and 115 controls were assessed by high-throughput deep sequencing (HiSeq. 2000, Illumina) and the Human Gene 1,1 ST microarray (Affymetrix), respectively. The analyses of differential expression for miRNA and mRNA were carried out separately applying Linear Model Fit using the Limma R package. ROC curves were used to evaluate the accuracy of the differentially expressed miRNAs in discriminating patients with ADHD from controls in an independent sample of 46 cases and 46 controls. In order to build miRNA-mRNA interaction networks that may be relevant to ADHD, including positive and negative relationships, we integrated the expression data of miRNAs and mRNAs differentially expressed in ADHD (adjusted p-values Results After quality control, normalization and background correction, a total of 573 miRNAs and 19,784 transcripts were included in the analysis. We identified a total of 79 miRNAs and 1,592 transcripts differentially expressed in ADHD when compared to controls. Of them, miR-191-5p and miR-23a-5p showed values of AUC > 0.70 in the test sample; they were selected for the subsequent correlation analysis. Evidence for 126 miRNA-mRNA pairs was found (p Discussion In conclusion, our findings provide for the first time tentative evidence for the contribution of miR-23a-5p - OCIAD2 correlated network to ADHD etiology through a comprehensive differentially expression analysis of miRNA and mRNA in PMBCs.

Genome-wide differential mRNA expression profiles in follicles of two breeds and at two stages of estrus cycle of gilts

Estrus expression by gilts and sows is hereditable and important for heat detection. To better understand the molecular biological mechanisms of estrus expression in gilts, the mRNA expression profiles of follicular tissue from Large White gilts in diestrus (LD, n = 3) and estrus (LE, n = 3), and Chinese indigenous Mi gilts in diestrus (MD, n = 2) and estrus (ME, n = 3) were investigated using RNA sequencing. We detected 122,804-335,295 SNPs, 6,140-14,947 InDel and 12 types of AS events (39.57% TSS, 34.90% TTS) in 11 samples. A total of 2,838 differentially expressed genes (DEGs) were found in LD vs MD, LE vs ME, LE vs LD, or ME vs MD comparisons. Two DEGs (ACP5 and PIGS) were observed in all comparisons. Two new genes (ENSSSCG00000028235 and ENSSSCG00000021903) were exclusively expressed in Mi and Large White gilts, respectively. Bioinformatics analyses indicate that these DEGs are involved in single-organism process, catalytic activity, cell adhesion and enriched in ECM-receptor interaction, olfactory transduction, ovarian steroidogenesis, steroid biosynthesis and CAMs signaling pathways. These results of RNA-Seq have provided important information for screening the key functional genes or molecular markers of estrus expression in gilts.

The CREB Transcription Factor Controls Transcriptional Activity of the Human RIC8B Gene.

Proper regulation of gene expression is essential for normal development, cellular growth, and differentiation. Differential expression profiles of mRNA coding for vertebrate Ric-8B during embryo and adult stages have been observed. In addition, Ric-8B is expressed in few cerebral nuclei subareas. These facts point to a dynamic control of RIC8B gene expression. In order to understand the transcriptional regulation of this gene, we searched for cis-elements in the sequence of the human RIC8B promoter region, identifying binding sites for the basic/leucine zipper (bZip) CREB transcription factor family (CRE sites) and C/EBP transcription factor family (C/EBP sites). CRE sites were found clustered near the transcription start site, while the C/EBP sites were found clustered at around 300 bp upstream the CRE sites. Here, we demonstrate the ability of CREB1 and C/EBPβ to bind their respective elements identified in the RIC8B promoter. Comparative protein-DNA interaction analyses revealed only the proximal elements as high affinity sites for CREB1 and only the distal elements as high affinity sites for C/EBPβ. Chromatin immunoprecipitation analyses, carried out using a human neuroblastoma cell line, confirmed the preferential association of CREB to the proximal region of the RIC8B promoter. By performing luciferase reporter assays, we found the CRE sites as the most relevant elements for its transcriptional activity. Taken together, these data show the existence of functional CREB and C/EBP binding sites in the human RIC8B gene promoter, a particular distribution of these sites and demonstrate a relevant role of CREB in stimulating transcriptional activity of this gene. J. Cell. Biochem. 117: 1797-1805, 2016. © 2016 Wiley Periodicals, Inc.

ANGI-08RADIOGENOMIC rCBV-IMAGING VISUALIZES THE DISTINCT ANGIOGENESIS TRANSCRIPTOME SIGNATURES OF IDH MUTANT AND WILD-TYPE GLIOMAS

BACKGROUND: The recent identification of isocitrate dehydrogenase (IDH) mutations in gliomas and several other cancers suggests that this pathway is involved in oncogenesis; however effector functions are complex and yet incompletely understood. To study the regulatory effects of IDH on hypoxia-inducible-factor 1-alpha (HIF1A), a driving force in hypoxia-initiated angiogenesis, we performed mRNA-expression and functional, as well as genotype/imaging phenotype correlation analysis. METHODS: We studied differential mRNA-expression profiles from 288 samples with low-grade and anaplastic gliomas from The Cancer Genome Atlas (TCGA) of HIF1A and related downstream signaling on a single-gene and pathway level, as well as upstream biological causes and probable downstream effects between mutant and wild-type IDH tumors. Genotype/imaging phenotype correlation analysis was performed in a separate (local) dataset with relative cerebral blood volume (rCBV) MRI - an estimate of tumor angiogenesis - in 73 treatment-naive patients with low-grade and anaplastic gliomas. RESULTS: We show decreased expression of HIF1A-target genes on a single-gene and pathway level, strong inhibition of upstream regulators such as HIF1A and downstream biological functions such as angio- and vasculogenesis in IDH-mutant tumors. Our radiogenomic imaging approach revealed increased levels of rCBV in IDH wild-type tumors, where a one-unit increase in rCBV corresponded to a two-third decrease in the odds for an IDH-mutation and correctly predicted IDH mutation status in 88% of patients. CONCLUSION: Together, these findings show that IDH-mutation status is associated with a distinct angiogenesis transcriptome signature which is non-invasively predictable with rCBV-imaging.

Proteomic analysis reveals that COP9 signalosome complex subunit 7A (CSN7A) is essential for the phase transition of migratory locust.

The migratory locust displays a reversible, density-dependent transition between the two phases of gregaria and solitaria. This phenomenon is a typical kind of behavior plasticity. Here, we report that COP9 signalosome complex subunit 7A (CSN7A) is involved in the regulation of locust phase transition. Firstly, 90 proteins were identified to express differentially between the two phases by quantitative proteomic analysis. Gregaria revealed higher levels in proteins related to structure formation, melanism and energy metabolism, whereas solitaria had more abundant proteins related to digestion, absorption and chemical sensing. Subsequently, ten proteins including CSN7A were found to reveal differential mRNA expression profiles between the two phases. The CSN7A had higher mRNA level in the gregaria as compared with the solitaria, and the mRNA amount in the gregaria decreased remarkably during the 32 h-isolation. However, the mRNA level in the solitaria kept constant during the crowding rearing. Finally and importantly, RNA interference of CSN7A in gregaria resulted in obvious phase transition towards solitaria within 24 h. It suggests that CSN7A plays an essential role in the transition of gregaria towards solitaria in the migratory locust. To our knowledge, it’s the first time to report the role of CSN in behavior plasticity of animals.

Differential mRNA expression profiles between hepatocellular carcinoma and adjacent normal liver tissue

Differential mRNA expression profiles between hepatocellular carcinoma and adjacent normal liver tissue

Changes in the Chondrocyte and Extracellular Matrix Proteome during Post-natal Mouse Cartilage Development

Skeletal growth by endochondral ossification involves tightly coordinated chondrocyte differentiation that creates reserve, proliferating, prehypertrophic, and hypertrophic cartilage zones in the growth plate. Many human skeletal disorders result from mutations in cartilage extracellular matrix (ECM) components that compromise both ECM architecture and chondrocyte function. Understanding normal cartilage development, composition, and structure is therefore vital to unravel these disease mechanisms. To study this intricate process in vivo by proteomics, we analyzed mouse femoral head cartilage at developmental stages enriched in either immature chondrocytes or maturing/hypertrophic chondrocytes (post-natal days 3 and 21, respectively). Using LTQ-Orbitrap tandem mass spectrometry, we identified 703 cartilage proteins. Differentially abundant proteins (q < 0.01) included prototypic markers for both early and late chondrocyte differentiation (epiphycan and collagen X, respectively) and novel ECM and cell adhesion proteins with no previously described roles in cartilage development (tenascin X, vitrin, Urb, emilin-1, and the sushi repeat-containing proteins SRPX and SRPX2). Meta-analysis of cartilage development in vivo and an in vitro chondrocyte culture model (Wilson, R., Diseberg, A. F., Gordon, L., Zivkovic, S., Tatarczuch, L., Mackie, E. J., Gorman, J. J., and Bateman, J. F. (2010) Comprehensive profiling of cartilage extracellular matrix formation and maturation using sequential extraction and label-free quantitative proteomics. Mol. Cell. Proteomics 9, 1296-1313) identified components involved in both systems, such as Urb, and components with specific roles in vivo, including vitrin and CILP-2 (cartilage intermediate layer protein-2). Immunolocalization of Urb, vitrin, and CILP-2 indicated specific roles at different maturation stages. In addition to ECM-related changes, we provide the first biochemical evidence of changing endoplasmic reticulum function during cartilage development. Although the multifunctional chaperone BiP was not differentially expressed, enzymes and chaperones required specifically for collagen biosynthesis, such as the prolyl 3-hydroxylase 1, cartilage-associated protein, and peptidyl prolyl cis-trans isomerase B complex, were down-regulated during maturation. Conversely, the lumenal proteins calumenin, reticulocalbin-1, and reticulocalbin-2 were significantly increased, signifying a shift toward calcium binding functions. This first proteomic analysis of cartilage development in vivo reveals the breadth of protein expression changes during chondrocyte maturation and ECM remodeling in the mouse femoral head.

Gene expression profiling reveals multiple differences in platelets from patients with stable angina or non-ST elevation acute coronary syndrome

Introduction Platelets play a key role in coronary artery disease. They have the capacity of protein synthesis through translation of megakaryocyte-derived mRNAs, which may influence pathophysiological functions. The present study aimed to prove the concept that platelets from patients with non-ST elevation acute coronary syndrome (NSTE-ACS) have differential mRNA expression profiles, in the hypothesis that this may influence their thrombogenicity. Materials and Methods Gene expression profiles were determined in RNA pools from resting platelets of patients with stable angina (SA, n = 14) or NSTE-ACS (n = 15) using a glass microarray platform. Validation was done by real-time PCR and immunoblot analyses in independent sets of individual samples (26 SA and 17 NSTE-ACS patients, in total). Parallel comparison with healthy subjects was performed to relate the relative abundance of validated genes in CAD patients to a control expression level. Results Microarray analysis identified 45 transcripts with a significant ≥ ± 2.0-fold difference in expression between NSTE-ACS and SA platelet pools. Thus, gene expression profiles at least partially discriminate unstable from stable CAD. Validation confirmed a significant over-expression of 3 genes in NSTE-ACS at both mRNA and protein level. In particular, the glycoprotein Ib β-polypeptide (GP1BB) was increased in NSTE-ACS also in comparison with healthy subjects. Conclusion This study provides evidence that NSTE-ACS platelets are potentially preconditioned to a higher degree of reactivity on the transcriptional level. Our data suggest that a different composition of the mRNA pool might mediate an increased platelet prothrombotic potential in NSTE-ACS patients.

Differential mRNA expression profiles in proximal tibia of aged rats in response to ovariectomy and low-Ca diet

Both ovariectomized animals and animals fed with Ca-depleted diets are commonly used in vivo models for the investigation of osteoporosis-related bone loss. The present study aimed to study the genomic responses of bone in aged female rats to ovariectomy and dietary Ca deficiency in these models. Aged (11 months old) Sprague–Dawley rats were subjected to bilateral ovariectomy or sham-operation and fed with diets containing different dietary Ca content (LCD, 0.1% Ca or HCD, 1.2% Ca) for 12 weeks. Serum and urine were collected for biochemical marker measurement, and tibias were collected for bone mineral density (BMD) analysis by pQCT as well as for gene expression analysis by real-time PCR. Ovariectomy increased serum N-telopeptides of bone type I collagen (NTx) levels in aged rats fed with HCD ( P < 0.05). In addition, ovariectomy reduced BMD and predicted bone strength of tibial proximal metaphysis in aged rats fed with either LCD or HCD. Dietary Ca deficiency did not alter serum bone-specific alkaline phosphatase (BAP) or NTx levels, but induced a loss of BMD at tibia proximal metaphysis in aged rats. Ovariectomy promoted the mRNA expression of alpha- 1 type I collagen (COL), osteoprotegerin (OPG) and receptor activator of nuclear factor-kappa B ligand (RANKL); and inhibited the mRNA expression of cathepsin K and matrix metalloproteinase-9 (MMP-9) in the proximal tibia of aged rats. Low-Ca diet significantly up-regulated the mRNA expression of COL, core binding factor I (Cbfa1), OPG and carbonic anhydrase II (CAII) in proximal tibia of aged rats. Our study revealed that the genomic responses of bone in proximal tibia to ovariectomy and dietary Ca deficiency were different. The bone loss induced by ovariectomy appears to be mediated primarily by an increase in RANKL mRNA expression; whereas the induction by dietary Ca restriction might be mediated by the induction of carbonic anhydrase II expression.