Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Chicken embryonic cerebral cortex exposed to two doses of PFHxS.

ABSTRACT: In a recent egg injection study, we showed that in ovo exposure to perfluorohexane sulfonate (PFHxS) affects the pipping success of developing chicken (Gallus gallus domesticus) embryos. We also found evidence of thyroid hormone (TH) pathway interference at multiple levels of biological organization (i.e. somatic growth, mRNA expression and circulating free thyroxine levels). Based on these findings, we hypothesize that PFHxS exposure interferes with TH-dependent neurodevelopmental pathways. The present study investigates global transcriptional profiles of cerebral cortex tissue from chicken embryos following exposure to a solvent control, 890 or 38,000 ng PFHxS/g egg (n=4-5 per group); doses which lead to the adverse effects above. PFHxS significantly alters the expression (≥1.5-fold, p≤0.001) of 11 transcripts at the low dose (LD; 890 ng/g) and 101 transcripts at the high dose (HD; 38,000 ng/g). Functional enrichment analysis shows that PFHxS affects genes involved in tissue development and morphology, cellular assembly and organization, and cell-to-cell signalling. Pathway and interactome analyses suggest that genes may be affected through several potential regulatory molecules, including integrin receptors, myelocytomatosis viral oncogene and CCAAT/enhancer binding protein. This study identifies key functional and regulatory modes of PFHxS action involving TH-dependent and -independent neurodevelopmental pathways. Some of these TH-dependent mechanisms that occur during embryonic development include tight junction formation, signal transduction and integrin signaling, while TH-independent mechanisms include gap junction intercellular communication. Reference Design. Reference = pool of equal parts of all control and treated samples. Control groups and 2 treatment groups. Control samples were chicken embryonic cerebral cortex exposed DMSO only (solvent). Treatments were: chicken embryonic cerebral cortex exposed to 890 ng/g PFHxS (LD) and 38,000 ng/g PFHxS (HD).

ORGANISM(S): Gallus gallus

SUBMITTER: Cristina Cassone

PROVIDER: E-GEOD-37339 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a better understanding of traits important to both humans and other animals. To detect chicken CNVs, we genotyped 475 animals derived from two broiler chicken lines divergently selected for abdominal fat content using chicken 60K SNP array, which is a high-throughput method widely used in chicken genomics studies. Results: Using PennCNV algorithm, we detected 438 and 291 CNVs in the lean and fat lines, respectively, corresponding to 271 and 188 CNV regions (CNVRs), which were obtained by merging overlapping CNVs. Out of these CNVRs, 99% were confirmed also by the CNVPartition program. These CNVRs covered 40.26 and 30.60 Mb of the chicken genome in the lean and fat lines, respectively. Moreover, CNVRs included 176 loss, 68 gain and 27 both (i.e. loss and gain within the same region) events in the lean line, and 143 loss, 25 gain and 20 both events in the fat line. Ten CNVRs were chosen for the validation experiment using qPCR method, and all of them were confirmed in at least one qPCR assay. We found a total of 886 genes located within these CNVRs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed they could play various roles in a number of biological processes. Integrating the results of CNVRs, known quantitative trait loci (QTL) and selective sweeps for abdominal fat content suggested that some genes (including SLC9A3, GNAL, SPOCK3, ANXA10, HELIOS, MYLK, CCDC14, SPAG9, SOX5, VSNL1, SMC6, GEN1, MSGN1 and ZPAX) may be important for abdominal fat deposition in the chicken. Conclusions: Our study provided a genome-wide CNVR map of the chicken genome, thereby contributing to our understanding of genomic structural variations and their potential roles in abdominal fat content in the chicken. In total, 475 birds (203 and 272 individuals from the lean and fat lines, respectively) from the 11th generation population of Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) were used. These 475 birds were genotyped by the chicken 60k SNP chip and PennCNV method were used to perform genome-wide CNV detection.

Project description:MicroRNA (miRNA) is a family of small regulatory RNA that post-transcriptionally regulates many biological functions including growth and development. Chicken miR-143 and miR-10a are expressed in both the embryonic and post-hatch chick in a spatio-temporal manner. In order to study the functions of these miRNAs, loss of function and microarray approaches were employed. Spleen cells were isolated from embryonic day 18 chickens and immediately transfected with either a synthetic miR-143 inhibitor or a synthetic miR-10a inhibitor or a negative control oligo-nucleotide (Dharmacon). Cultures were maintained for 48 hrs and microarray analysis was performed using the Arizona Gallus gallus 20.7K long oligoarray (GPL6049). Differentially expressed genes were identified for each miRNA by comparing the miRNA knock-down group to the negative control group. The differentially expressed genes were functionally categorized using the DAVID Functional Annotation Tool (http://david.abcc.ncifcrf.gov/). The 3â-UTR of the up-regulated genes (de-repressed after the miRNAs knock-down) were scanned for potential miR-143 or miR-10a binding sites using the miRanda algorithm version 3.1 (http://www.microrna.org/microrna). In addition, the Chicken (Gallus gallus) Unigene database (NCBI) was also used to predict potential targets of these miRNAs. A set of predicted targets for both miRNAs was selected and validated by dual luciferase reporter gene assay. Overall, many of the identified targets for miR-143 are associated with cell proliferation, tumerigenesis and apoptosis. Many of potential targets for miR-10a are associated with immune response. A reference designed microarray was performed in which samples (Cy3) were co-hybridized with the reference RNA pool (Cy5) on the array. The microarray data set was processed using within- and across-array loess normalization method in JMP Genomics 3.0, SAS (Cary, NC). Data quality was evaluated using the MA plots process and the correlation and grouped scatter plots procedure (JMP Genomics 3.0). Differentially expressed genes were identified using ANOVA process on JMP Genomics 3.0 with fixed effect of treatments and random effect of arrays.

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Chicken embryonic cerebral cortex exposed to two doses of PFHxS.

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