Genome Microarray Research Articles

Radiation dose-rate effects on gene expression for human biodosimetry.

BackgroundThe effects of dose-rate and its implications on radiation biodosimetry methods are not well studied in the context of large-scale radiological scenarios. There are significant health risks to individuals exposed to an acute dose, but a realistic scenario would include exposure to both high and low dose-rates, from both external and internal radioactivity. It is important therefore, to understand the biological response to prolonged exposure; and further, discover biomarkers that can be used to estimate damage from low-dose rate exposures and propose appropriate clinical treatment.MethodsWe irradiated human whole blood ex vivo to three doses, 0.56 Gy, 2.23 Gy and 4.45 Gy, using two dose rates: acute, 1.03 Gy/min and a low dose-rate, 3.1 mGy/min. After 24 h, we isolated RNA from blood cells and these were hybridized to Agilent Whole Human genome microarrays. We validated the microarray results using qRT-PCR.ResultsMicroarray results showed that there were 454 significantly differentially expressed genes after prolonged exposure to all doses. After acute exposure, 598 genes were differentially expressed in response to all doses. Gene ontology terms enriched in both sets of genes were related to immune processes and B-cell mediated immunity. Genes responding to acute exposure were also enriched in functions related to natural killer cell activation and cell-to-cell signaling. As expected, the p53 pathway was found to be significantly enriched at all doses and by both dose-rates of radiation. A support vectors machine classifier was able to distinguish between dose-rates with 100 % accuracy using leave-one-out cross-validation.ConclusionsIn this study we found that low dose-rate exposure can result in distinctive gene expression patterns compared with acute exposures. We were able to successfully distinguish low dose-rate exposed samples from acute dose exposed samples at 24 h, using a gene expression-based classifier. These genes are candidates for further testing as markers to classify exposure based on dose-rate.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-015-0097-x) contains supplementary material, which is available to authorized users.

Cross talk between cytokine and hyperthermia-induced pathways: identification of different subsets of NF-κB-dependent genes regulated by TNFα and heat shock.

Heat shock inhibits NF-κB signaling, yet the knowledge about its influence on the regulation of NF-κB-dependent genes is limited. Using genomic approaches, i.e., expression microarrays and ChIP-Seq, we aimed to establish a global picture for heat shock-mediated impact on the expression of genes regulated by TNFα cytokine. We found that 193 genes changed expression in human U-2 osteosarcoma cells stimulated with cytokine (including 77 genes with the κB motif in the proximal promoters). A large overlap between sets of genes modulated by cytokine or by heat shock was revealed (86 genes were similarly affected by both stimuli). Binding sites for heat shock-induced HSF1 were detected in regulatory regions of 1/3 of these genes. Furthermore, pre-treatment with heat shock affected the expression of 2/3 of cytokine-modulated genes. In the largest subset of co-affected genes, heat shock suppressed the cytokine-mediated activation (antagonistic effect, 83 genes), which genes were associated with the canonical functions of NF-κB signaling. However, subsets of co-activated and co-repressed genes were also revealed. Importantly, pre-treatment with heat shock resulted in the suppression of NF-κB binding in the promoters of the cytokine-upregulated genes, either antagonized or co-activated by both stimuli. In conclusion, we confirmed that heat shock inhibited activation of genes involved in the classical cytokine-mediated functions of NF-κB. On the other hand, genes involved in transcription regulation were over-represented in the subset of genes upregulated by both stimuli. This suggests the replacement of NF-κB-mediated regulation by heat shock-mediated regulation in the latter subset of genes, which may contribute to the robust response of cells to both stress conditions.Electronic supplementary materialThe online version of this article (doi:10.1007/s00438-015-1055-1) contains supplementary material, which is available to authorized users.

PP05.5 – 3064: The role of exome sequencing in daily pediatric neurology practice

Objective Pediatric neurologists aim to provide a swift and precise diagnosis and an appropriate treatment and/or supportive care procedure for children with more than a 1000 disorders of the brain, spinal cord, nerves and/or muscles. Finding a diagnosis however in many cases is not easy, not fast, not cheap and often involves burdensome procedures. Could we lower the burden and rise the diagnostic yield bij using whole exome sequencing? Methods We selected 50 patients entering the pediatric neurology department of our hospital with complicated but nonspecific clinical features with a presumed genetic origin of their disease (like developmental delay, neurodegenerative diseases, brain malformation, movement disorder, neuromuscular disease, severe epilepsy). They received standard pediatric neurology care and investigations like MRI, genomic microarray, a gene specific Sanger sequencing test, metabolic testing or muscle biopsy. Parallel to the standard care pathway, the same 50 patients were simultaneously tested using whole exome sequencing. The exome data of each patient was analysed for single nucleotide variants and insertion/deletion events, and copy number variation (CNVs) >200 kb in size. We compared both groups for diagnostic yield, health care costs and parents satisfaction. Results 50 patients (28 females, 22 males, age range 4 months–16 years) entered the study. Three patients (6%) received a conclusive genetic diagnosis in the standard care arm. In total, 28 de novo SNVs were identified, including 2 insertion/deletion events and 26 point mutations using whole exome sequencing. 10 of them were known disease causing SNVs, the other 18 where highly suspected to be pathogenic. The average costs per patient were €12,241 in the standard care, the costs of WES are currently €3,600. Conclusion Whole exome sequencing has al higher yield and lower costs to provide a diagnosis in child presumed to have a genetic origin of their disease Pediatric neurologists aim to provide a swift and precise diagnosis and an appropriate treatment and/or supportive care procedure for children with more than a 1000 disorders of the brain, spinal cord, nerves and/or muscles. Finding a diagnosis however in many cases is not easy, not fast, not cheap and often involves burdensome procedures. Could we lower the burden and rise the diagnostic yield bij using whole exome sequencing? We selected 50 patients entering the pediatric neurology department of our hospital with complicated but nonspecific clinical features with a presumed genetic origin of their disease (like developmental delay, neurodegenerative diseases, brain malformation, movement disorder, neuromuscular disease, severe epilepsy). They received standard pediatric neurology care and investigations like MRI, genomic microarray, a gene specific Sanger sequencing test, metabolic testing or muscle biopsy. Parallel to the standard care pathway, the same 50 patients were simultaneously tested using whole exome sequencing. The exome data of each patient was analysed for single nucleotide variants and insertion/deletion events, and copy number variation (CNVs) >200 kb in size. We compared both groups for diagnostic yield, health care costs and parents satisfaction. 50 patients (28 females, 22 males, age range 4 months–16 years) entered the study. Three patients (6%) received a conclusive genetic diagnosis in the standard care arm. In total, 28 de novo SNVs were identified, including 2 insertion/deletion events and 26 point mutations using whole exome sequencing. 10 of them were known disease causing SNVs, the other 18 where highly suspected to be pathogenic. The average costs per patient were €12,241 in the standard care, the costs of WES are currently €3,600. Whole exome sequencing has al higher yield and lower costs to provide a diagnosis in child presumed to have a genetic origin of their disease

Significantly reduced function of T cells in patients with acute arterial thrombosis.

ObjectivesTo explore the intrinsic factors related to the pathogenesis of acute arterial thrombosis (AAT) and to elucidate the pathogenesis of AAT on the basis of differentially expressed genes.MethodsPatients with acute myocardial infarction (AMI), stable angina (SA) and healthy controls (n = 20 per group) were recruited, and the whole human genome microarray analysis was performed to detect the differentially expressed genes among these subjects.ResultsPatients with AMI had disease-specific gene expression pattern. Biological functional analysis showed the function of T cells was significantly reduced, the mitochondrial metabolism significantly decreased, the ion metabolism was abnormal, the cell apoptosis and inflammatory reaction increased, the phagocytosis elevated, the neutrophil-mediated immunity increased and the post-traumatic repair of cells and tissues increased in AMI patients. The biological function in SA group and healthy controls remained stable and was comparable.ConclusionsThe reduced function of T cell gene models in AAT showed the dysfunction of the immune system. The pathogenesis of AAT may be related to the inflammatory reaction after arterial intima infection caused by potential pathogenic microorganisms.

Development of a Custom-Designed, Pan Genomic DNA Microarray to Characterize Strain-Level Diversity among Cronobacter spp.

Cronobacter species cause infections in all age groups; however neonates are at highest risk and remain the most susceptible age group for life-threatening invasive disease. The genus contains seven species:Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite an abundance of published genomes of these species, genomics-based epidemiology of the genus is not well established. The gene content of a diverse group of 126 unique Cronobacter and taxonomically related isolates was determined using a pan genomic-based DNA microarray as a genotyping tool and as a means to identify outbreak isolates for food safety, environmental, and clinical surveillance purposes. The microarray constitutes 19,287 independent genes representing 15 Cronobacter genomes and 18 plasmids and 2,371 virulence factor genes of phylogenetically related Gram-negative bacteria. The Cronobacter microarray was able to distinguish the seven Cronobacter species from one another and from non-Cronobacter species; and within each species, strains grouped into distinct clusters based on their genomic diversity. These results also support the phylogenic divergence of the genus and clearly highlight the genomic diversity among each member of the genus. The current study establishes a powerful platform for further genomics research of this diverse genus, an important prerequisite toward the development of future countermeasures against this foodborne pathogen in the food safety and clinical arenas.

Bmi-1 expression modulates non-small cell lung cancer progression

Previous studies indicate that the role of B lymphoma Mo-MLV insertion region 1 homolog (Bmi-1) is responsible for multiple cancer progression. However, Bmi-1 in controlling gene expression in non-small cell lung cancer (NSCLC) development is not well explored. Here we report that the Bmi-1 level is highly increased in primary NSCLC tissues compared to matched adjacent non-cancerous tissues and required for lung tumor growth in xenograft model. Furthermore, we also demonstrate that Bmi-1 level is lower in matched involved lymph node cancerous tissues than the respective primary NSCLC tissues. We find that Bmi-1 does not affect cell cycle and apoptosis in lung cancer cell lines as it does not affect the expression of p16/p19, Pten, AKT and P-AKT. Mechanistic analyses note that reduction of Bmi-1 expression inversely regulates invasion and metastasis of NSCLC cells in vitro and in vivo, followed by induction of epithelial-mesenchymal transition (EMT). Using genome microarray assays, we find that RNAi-mediated silence of Bmi-1 modulates some important molecular genetics or signaling pathways, potentially associated with NSCLC development. Taken together, our findings disclose for the first time that Bmi-1 level accumulates strongly in early stage and then declines in late stage, which is potentially important for NSCLC cell invasion and metastasis during progression.

Anticancer activity of galactoxyloglucan polysaccharide-conjugated doxorubicin nanoparticles: Mechanistic insights and interactome analysis

Toxicity associated with chemotherapeutic drugs such as doxorubicin (Dox), is one of the major obstacles that is currently affecting patients. PST-Dox (Galactoxyloglucan, PST001-conjugated Dox) nanoparticles were synthesized by encapsulating Dox with polysaccharide PST001, isolated from Tamarindus indica (Ti) by ionic gelation with tripolyphosphate (TPP). Herein, we demonstrate a detailed mechanistic and interactome network analysis that is specific to PST-Dox action in cancer cells and normal lymphocytes. Our results show that PST-Dox is superior to its parental counterparts, exhibiting a greater cytotoxicity by the induction of apoptosis against a wide variety of cancers by enhanced cellular uptake of Dox from the nanoparticle conjugates. Also, PST-Dox nanoparticles were non-toxic to normal lymphocytes with limited immunostimulatory effects up to certain doses. Elucidation of molecular mechanism by whole genome microarray in cancer cells and lymphocytes revealed that a large number of genes were dysregulated specifically in cancer cells. Specifically, a unique target gene EGR1, contextually determined translational activation of P53 in the cancerous and non-cancerous cells. Most of the key downregulated genes were tyrosine kinases, indicating the potential inhibitory action of PST-Dox on tyrosine kinase oncogenic pathways. Western blotting of proteins corresponding to the genes that were altered at the genomic level was very well correlated in the majority of them, except in a few that demonstrated post-transcriptional modifications. The important findings and highly disciplined approaches highlighted in the present study will speed up the therapeutic potential of this augmented nanoparticle formulation for more robust clinical studies and testing in several cancers.

Microarray gene expression analysis reveals major differences between Toxocara canis and Toxocara cati neurotoxocarosis and involvement of T. canis in lipid biosynthetic processes

Toxocara canis and Toxocara cati are globally occurring intestinal nematodes of dogs and cats with a high zoonotic potential. Migrating larvae in the CNS of paratenic hosts, including humans, may cause neurotoxocarosis resulting in a variety of neurological symptoms. Toxocara canis exhibits a stronger affinity to the CNS than T. cati, causing more severe neurological symptoms in the mouse model. Pathomechanisms of neurotoxocarosis as well as host responses towards the respective parasite are mostly unknown. Therefore, the aim of this study was to characterise the pathogenesis at a transcriptional level using whole genome microarray expression analysis and identify differences and similarities between T. canis- and T. cati-infected brains. Microarray analysis was conducted in cerebra and cerebella of infected C57Bl/6J mice 42daysp.i. revealing more differentially transcribed genes for T. canis- than T. cati-infected brains. In cerebra and cerebella of T. canis-infected mice, a total of 2304 and 1954 differentially transcribed genes, respectively, were identified whereas 113 and 760 differentially transcribed genes were determined in cerebra and cerebella of T. cati-infected mice. Functional annotation analysis revealed major differences in host responses in terms of significantly enriched biological modules. Up-regulated genes were mainly associated with the terms “immune and defence response”, “sensory perception” as well as “behaviour/taxis” retrieved from the Gene Ontology database. These observations indicate a strong immune response in both infection groups with T. cati-infected brains revealing less severe reactions. Down-regulated genes in T. canis-infected cerebra and cerebella revealed a significant enrichment for the Gene Ontology term “lipid/cholesterol biosynthetic process”. Cholesterol is a highly abundant and important component in the brain, representing several functions. Disturbances of synthesis as well as concentration changes may lead to dysfunction in signal transduction and neurodegenerative disease. Overall, only a minor overlap of differentially transcribed genes was observed between the two infection groups in both brain parts. Most genes are regulated individually in each infection group, supporting the evident differences of both roundworm species observed in the paratenic host in previous studies. In summary the present study underlines the differences in pathogenicity of T. canis and T. cati. It furthermore provides a comprehensive basis for future analyses over the course of infection as well as functional tests to identify gene regulatory circuits that are crucial for pathogenesis of neurotoxocarosis. The results of this study provide a promising foundation for further specific research to evaluate the particular pathogenetic mechanisms and to identify possible therapeutic targets.

Transcriptomic signatures in whole blood of patients who acquire a chronic inflammatory response syndrome (CIRS) following an exposure to the marine toxin ciguatoxin.

BackgroundCiguatoxins (CTXs) are polyether marine neurotoxins found in multiple reef-fish species and are potent activators of voltage-gated sodium channels. It is estimated that up to 500,000 people annually experience acute ciguatera poisoning from consuming toxic fish and a small percentage of these victims will develop a chronic, multisymptom, multisystem illness, which can last years, termed a Chronic Inflammatory Response Syndrome (CIRS). Symptoms of ciguatera CIRS include fatigue, cognitive deficits, neurologic deficits, pain and sensitivity to light. There are few treatment options for ciguatera CIRS since little is known about its pathophysiology.MethodsThis study characterizes the transcriptional profile in whole blood of 11 patients with ciguatera-induced CIRS and 11 normal controls run in duplicate using Agilent one color whole genome microarrays. Differential expression was determined by using a combination of moderated t-test p-value and fold change (FC). Significant genes were subjected to gene ontology, principal component analysis and SVM classification. Seven significant genes found by microarray were validated by PCR.ResultsUsing a low stringency (p < 0.05 and FC > 1.4) and a high stringency (p < 0.01 and FC > 1.5) filter, the resulting gene sets of 185 and 55, respectively, showed clear separation of cases and controls by PCA as well as 100% classification accuracy by SVM, indicating that the gene profiles can separate patients from controls. PCR results of 7 genes showed a 95% correlation to microarray data. Several genes identified by microarray are important in wound healing (CD9, CD36, vWF and Factor XIII), adaptive immunity (HLA-DQB1, DQB2, IL18R1 and IL5RA) and innate immunity (GZMK, TOLLIP, SIGIRR and VIPR2), overlapping several areas shown to be disrupted in a mouse model of acute exposure to ciguatoxin. Another area of interest was differential expression of long, non-coding sequences, or lncRNA.ConclusionsDisruptions of innate and adaptive immune mechanisms were recorded at both the genomic and proteomic level. A disruption in the HLA-T cell receptor axis could indicate HLA haplotype sensitivity for this chronic syndrome, as noted in many autoimmune conditions. Taken together, these indicators of illness provide additional insights into pathophysiology and potential therapies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-015-0089-x) contains supplementary material, which is available to authorized users.

Genome wide expression analysis of the effect of Socheongryong Tang in asthma model of mice

ObjectiveTo investigate the molecular effect of Socheongryong Tang (SCRT, Xiaoqinglong Tang in Chinese) on whole genome level in asthma mouse model by microarray technology. MethodsAsthma was induced by intranasal instillation of ovalbumin in mouse. After administration of SCRT on asthma-induced mouse, the expression of genes in lung tissue was measured using whole genome microarray. The functional implication of differentially expressed genes was performed using ontological analysis and the similarity of promoter structure of genes was also analyzed. ResultsTreatment of SCRT restored expression level of many up- or down-regulated genes in asthma model, and this recovery rate means SCRT could regulate a set of genes having specific TFBS binding sites. ConclusionIn this study, we identified a set of genes subjected to similar regulation by SCRT in asthma model in mice.

Cardiac mRNA Expression in Inbred Rat Strains Divergent in Survival Time after Hemorrhage

We previously identified inbred rat strains differing in survival time after severe controlled hemorrhage (StaH). To identify early biomarkers of hemorrhagic shock and genes that might explain differences in STaH, rats from three strains [Brown Norway (BN); Dark Agouti (DA), and Fawn Hooded Hypertensive (FHH)] with different StaH (DA = FHH > BN; 4-5 rats/group) were assigned to one of three treatment groups: non-operated controls (CNTL), surgically catheterized rats (CATH), or rats catheterized and bled (~46% hemorrhage) 24 h post-surgery (BLD). Rats were euthanized 30 min after handling or 30 min after start of a 26 min bleed. After euthanasia, hearts were removed and frozen in liquid nitrogen. Total RNA was isolated, fluorescently labeled, hybridized to Agilent rat whole genome microarrays, and statistically analyzed with BRB Array Tools. After controlling for multiple comparisons via the False Discovery Rate (<10%), mRNA expression for 65 known genes differed (P<.01). There were no inbred rat strain-related differences in mRNA expression (P>.05). Expression of 26 genes changed after BLD (20 decreased, 6 increased). These changes ranged from 5 to 556-fold. Genes with hemorrhage-associated changes included: Hif1α (22-fold decrease; oxygen homeostasis); Map4 (45-fold decrease; mitochondrial permeabilization); Mmp21 (24-fold decrease; Ca++ binding); Tubb5 (556-fold decrease; phagocytosis and protein complex binding); and Rnase10 (70-fold increase; nucleic acid binding). In the absence of inbred rat strain differences in mRNA expression, our data do not identify cardiac genes associated with differences in STaH. However, the data do provide new information concerning cardiac mRNA expression that rapidly changes after hemorrhage. Funding: US Army MRMC.

Analysis of RVLM Gene Expression in Young, Middle‐Aged and Aged F344 Rats

Abstract: The rostral ventral lateral medulla (RVLM) plays a critical role in regulation of basal sympathetic nerve discharge (SND). Advanced age is associated with altered regulation of SND, however, the effect of age on central medullary mechanisms regulating SND remains unknown. A series of experiments were initiated to identify cellular and molecular targets that may mediate age‐related changes in medullary regulation of SND. We tested the hypothesis that aging shifts the balance of RVLM excitatory and inhibitory influences towards excitation. Gene expression analysis was performed using Agilent Whole Rat Genome Microarray 4×44K followed by validation of microarray with TaqMan real‐time RT‐PCR and immunoblotting for specific RVLM proteins. Total RNA and protein were extracted from RVLM micropunches from young, middle‐aged and aged F344 rats. Microarray analysis revealed up‐regulation in aged compared to young and middle‐aged rats of several genes related to immune function and neurotransmitter receptors. Specifically, the chemokines CCL3, CCL4 and CCL5 were up‐regulated 3 to 4 fold in aged rats compared to young and middle‐aged rats. The results of previous studies suggest that increased chemokines in the brain can modulate NMDA receptor responses. The current preliminary results suggest that increased chemokine gene expression in the RVLM of aged rats may contribute to age‐related changes in SND regulation. Supported by NIH A6‐041948.

Macrophage gene expression associated with remodeling of the prepartum rat cervix: microarray and pathway analyses.

As the critical gatekeeper for birth, prepartum remodeling of the cervix is associated with increased resident macrophages (Mφ), proinflammatory processes, and extracellular matrix degradation. This study tested the hypothesis that expression of genes unique to Mφs characterizes the prepartum from unremodeled nonpregnant cervix. Perfused cervix from prepartum day 21 postbreeding (D21) or nonpregnant (NP) rats, with or without Mφs, had RNA extracted and whole genome microarray analysis performed. By subtractive analyses, expression of 194 and 120 genes related to Mφs in the cervix from D21 rats were increased and decreased, respectively. In both D21 and NP groups, 158 and 57 Mφ genes were also more or less up- or down-regulated, respectively. Mφ gene expression patterns were most strongly correlated within groups and in 5 major clustering patterns. In the cervix from D21 rats, functional categories and canonical pathways of increased expression by Mφ gene related to extracellular matrix, cell proliferation, differentiation, as well as cell signaling. Pathways were characteristic of inflammation and wound healing, e.g., CD163, CD206, and CCR2. Signatures of only inflammation pathways, e.g., CSF1R, EMR1, and MMP12 were common to both D21 and NP groups. Thus, a novel and complex balance of Mφ genes and clusters differentiated the degraded extracellular matrix and cellular genomic activities in the cervix before birth from the unremodeled state. Predicted Mφ activities, pathways, and networks raise the possibility that expression patterns of specific genes characterize and promote prepartum remodeling of the cervix for parturition at term and with preterm labor.

Single-nucleotide polymorphisms and haplotypes of non-coding area in the CP gene are correlated with Parkinson's disease.

Our previous studies have demonstrated that ceruloplasmin (CP) dysmetabolism is correlated with Parkinson's disease (PD). However, the causes of decreased serum CP levels in PD patients remain to be clarified. This study aimed to explore the potential association between genetic variants of the CP gene and PD. Clinical features, serum CP levels, and the CP gene (both promoter and coding regions) were analyzed in 60 PD patients and 50 controls. A luciferase reporter system was used to investigate the function of promoter single-nucleotide polymorphisms (SNPs). High-density comparative genomic hybridization microarrays were also used to detect large-scale copy-number variations in CP and an additional 47 genes involved in PD and/or copper/iron metabolism. The frequencies of eight SNPs (one intronic SNP and seven promoter SNPs of the CP gene) and their haplotypes were significantly different between PD patients, especially those with lowered serum CP levels, and controls. However, the luciferase reporter system revealed no significant effect of the risk haplotype on promoter activity of the CP gene. Neither these SNPs nor their haplotypes were correlated with the Hoehn and Yahr staging of PD. The results of this study suggest that common genetic variants of CP are associated with PD and further investigation is needed to explore their functions in PD.

Identification of early transcriptome signatures in placenta exposed to insulin and obesity

The purpose of this study was to investigate the effects of insulin on human placental transcriptome and biological processes in first-trimester pregnancy. Maternal plasma and placenta villous tissue were obtained at the time of voluntary termination of pregnancy (7-12 weeks) from 17 lean (body mass index, 20.9±1.5 kg/m2) and 18 obese (body mass index, 33.5±2.6 kg/m2) women. Trophoblast cells were immediately isolated for in vitro treatment with insulin or vehicle. Patterns of global gene expression were analyzed using genome microarray profiling after hybridization to Human Gene 1.1 ST and real time reverse transcription-polymerase chain reaction. The global trophoblast transcriptome was qualitatively separated in insulin-treated vs untreated trophoblasts of lean women. The number of insulin-sensitive genes detected in the trophoblasts of lean women was 2875 (P<.001). Maternal obesity reduced the number of insulin-sensitive genes recovered by 30-fold. Insulin significantly impaired several gene networks regulating cell cycle and cholesterol homeostasis but did not modify pathways related to glucose transport. Obesity associated with high insulin and insulin resistance, but not maternal hyperinsulinemia alone, impaired the global gene profiling of early gestation placenta, highlighting mitochondrial dysfunction and decreased energy metabolism. We report for the first time that human trophoblast cells are highly sensitive to insulin regulation in early gestation. Maternal obesity associated with insulin resistance programs the placental transcriptome toward refractoriness to insulin with potential adverse consequences for placental structure and function.

A novel Schistosoma japonicum endonuclease homologous to DNase II.

BackgroundRecent advances in studies of the Schistosoma japonicum genome have opened new avenues for the elucidation of parasite biology and the identification of novel targets for vaccines, drug development and early diagnostic tools.ResultsIn this study, we surveyed the S. japonicum genome database for genes encoding nucleases. A total of 130 nucleases of 3 classes were found. Transcriptional analysis of these genes using a genomic DNA microarray revealed that the majority of the nucleases were differentially expressed in parasites of different developmental stages or different genders, whereas no obvious transcriptional variation was detected in parasites from different hosts. Further analysis of the putative DNases of S. japonicum revealed a novel DNase II homologue (Sjda) that contained a highly conserved catalytic domain. A recombinant Sjda-GST protein efficiently hydrolysed genomic DNA in the absence of divalent iron. Western-blot and immunofluorescence assays showed that Sjda was mainly expressed on the teguments of female adult parasites and induced early humoral immune responses in infected mice.ConclusionsA novel DNase II homologue, Sjda, was identified in S. japonicum. Sjda was mainly distributed on the teguments of adult female parasites and possessed a typical divalent iron-independent DNA catalytic activity. This protein may play an important role in the host–parasite interaction.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1319-5) contains supplementary material, which is available to authorized users.

Progression risk assessments of individual non-invasive gastric neoplasms by genomic copy-number profile and mucin phenotype.

BackgroundEarly detection and treatment of non-invasive neoplasms can effectively reduce the incidence of advanced gastric carcinoma (GC), but only when the lineage is continuous between non-invasive and advanced tumours. Although a fraction of non-invasive neoplasms progress to invasive GC, it is difficult to identify individual progression-prone non-invasive neoplasms. To classify non-invasive gland-forming gastric neoplasms into clusters of different levels of progression risk, we applied mucin phenotyping and genomic DNA microarray analyses to intramucosal gland-forming gastric neoplasms.MethodsFormalin-fixed, paraffin-embedded tissues from 19 non-invasive and 24 invasive gland-forming neoplasms were obtained via endoscopic submucosal dissection or surgical excision. According to the Vienna classification, intramucosal neoplasms were classified as low-grade or high-grade non-invasive neoplasms (LGNs [category 3] and HGNs [category 4], respectively) or invasive carcinomas (intramucosal GCs and mucosal parts of submucosal or deeper GCs [category 5]). Neoplastic lesions were characterized by mucin phenotypes determined using monoclonal antibodies against MUC2, MUC5AC, MUC6, and CD10. Genomic DNA samples from mucosal neoplasms were subjected to array-based comparative genomic hybridization and subsequent unsupervised, hierarchical clustering with selected large-sized genes.ResultsThere was no significant difference in mucin phenotype between HGNs/LGNs and invasive carcinomas. The clustering classified samples into stable, unstable, and intermediate. The histological tumour grade or mucin phenotype of non-invasive neoplasms did not correlate with the clustering results. Each cluster may represent an independent lineage of different outcome because the size distribution of non-invasive tumours among the 3 clusters almost overlapped. In contrast, the unstable cluster alone included invasive carcinomas.ConclusionsThese findings suggest that the outcome of individual tumours is not stochastically determined but can be predicted from the genomic copy-number profile even at the non-invasive stage. Non-invasive neoplasms of the unstable clusters, which accounted for 21% of non-invasive neoplasms, may progress to invasive carcinomas, whereas those of stable cluster may not.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-015-0080-6) contains supplementary material, which is available to authorized users.

Genomic diversity of Clostridium difficile strains

Approaches to exploring Clostridium difficile genomic diversity have ranged from molecular typing methods to use of comparative genome microarrays and whole genome sequence comparisons. The C. difficile population structure is clonal and distributed into six clades, which correlate well with MLST STs (multilocus sequence types) and PCR ribotypes. However, toxigenic strains and strains with increased virulence are distributed throughout several clades. Here we summarize studies on C. difficile genomic diversity, with emphasis on phylogenetic aspects, epidemiological aspect and variability of some virulence factors.

Whole genome expression profiling of gastric high-grade intraepithelial neoplasia with or without cancer.

To investigate the whole genome expression profiles between gastric high-grade intraepithelial neoplasia (HGIN) tissues with cancer and HGIN tissues without cancer. Gastric specimens from an upper magnifying chromoendoscopic targeted biopsy were collected at Peking Union Medical College Hospital from March 2010 to May 2013. Each of the forceps biopsies from the 21 patients was HGIN,but there were 10 HGIN and 11 HGIN with cancer after the endoscopic submucosal dissection. The whole genome expression profiling was performed on 10 HGIN samples and 11 HGIN with cancer samples using Agilent 4 × 44K Whole Human Genome microarrays. Differentially expressed genes between different types of lesions were identified using an unpaired t-test and corrected with the Benjamini and Hochberg false discovery rate algorithm. A gene ontology(GO)enrichment analysis was performed using the GeneSpring software GX 12.6. The gene expression patterns were different between HGIN tissues with cancer and HGIN tissues without cancer. There were 470 significantly differentially expressed transcripts between them (P<0.05,Fold Change>2), with 180 up-regulated genes and 290 down-regulated genes in HGIN tissues with cancer. A GO enrichment analysis demonstrated that the most striking over-expressed transcripts in HGIN with cancer were in the category of triglyceride biosynthetic process,acylglycerol biosynthetic process,neutral lipid biosynthetic process,glycerol ether metabolic process,organic ether metabolic process,and glycerolipid metabolic process. The change of lipid metabolism may contribute to the pathogenesis of gastric cancer at an early stage.

Gene expression profile of human lung epithelial cells chronically exposed to single-walled carbon nanotubes.

A rapid increase in utility of engineered nanomaterials, including carbon nanotubes (CNTs), has raised a concern over their safety. Based on recent evidence from animal studies, pulmonary exposure of CNTs may lead to nanoparticle accumulation in the deep lung without effective clearance which could interact with local lung cells for a long period of time. Physicochemical similarities of CNTs to asbestos fibers may contribute to their asbestos-like carcinogenic potential after long-term exposure, which has not been well addressed. More studies are needed to identify and predict the carcinogenic potential and mechanisms for promoting their safe use. Our previous study reported a long-term in vitro exposure model for CNT carcinogenicity and showed that 6-month sub-chronic exposure of single-walled carbon nanotubes (SWCNT) causes malignant transformation of human lung epithelial cells. In addition, the transformed cells induced tumor formation in mice and exhibited an apoptosis resistant phenotype, a key characteristic of cancer cells. Although the potential role of p53 in the transformation process was identified, the underlying mechanisms of oncogenesis remain largely undefined. Here, we further examined the gene expression profile by using genome microarrays to profile molecular mechanisms of SWCNT oncogenesis. Based on differentially expressed genes, possible mechanisms of SWCNT-associated apoptosis resistance and oncogenesis were identified, which included activation of pAkt/p53/Bcl-2 signaling axis, increased gene expression of Ras family for cell cycle control, Dsh-mediated Notch 1, and downregulation of apoptotic genes BAX and Noxa. Activated immune responses were among the major changes of biological function. Our findings shed light on potential molecular mechanisms and signaling pathways involved in SWCNT oncogenic potential.Electronic supplementary materialThe online version of this article (doi:10.1186/s11671-014-0707-0) contains supplementary material, which is available to authorized users.