Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of mouse muscle tissue after in-vivo intramuscularly administration of MF59, CpG, MF59+CpG, alum and PBS

ABSTRACT: Analysis of whole mouse muscle gene expression signature induced by in-vivo intramuscularly administration of MF59, CpG, MF59+CpG, alum and PBS. MF59 and alum are licensed human vaccine adjuvants; CpG is a TLR-agonist adjuvant.

ORGANISM(S): Mus musculus

SUBMITTER: Mosca Flaviana

PROVIDER: E-TABM-506 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Molecular and cellular signatures of human vaccine adjuvants.

Mosca F F Tritto E E Muzzi A A Monaci E E Bagnoli F F Iavarone C C O'Hagan D D Rappuoli R R De Gregorio E E

Proceedings of the National Academy of Sciences of the United States of America 20080723 30

Oil-in-water emulsions are potent human adjuvants used for effective pandemic influenza vaccines; however, their mechanism of action is still unknown. By combining microarray and immunofluorescence analysis, we monitored the effects of the adjuvants MF59 oil-in-water emulsion, CpG, and alum in the mouse muscle. MF59 induced a time-dependent change in the expression of 891 genes, whereas CpG and alum regulated 387 and 312 genes, respectively. All adjuvants modulated a common set of 168 genes and ...[more]

PMID: 18650390

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Project description:RNA-baffsed vaccines have recently emerged as a promising alternative to the use of DNA-based and viral vector vaccines, in part due to the potential to simplify how vaccines are made and facilitate a rapid response to newly emerging infections. SAM vaccines are based on engineered self-amplifying mRNA (SAM) replicons encoding an antigen, formulated with a synthetic delivery system, and induce broad-based immune responses in preclinical animal models. BALB/c mice (three biological replicates per group) were injected bilaterally intramuscularly (i.m.) with 50 Î¼l per quadriceps of Phosphate Buffered Saline alone (Control group), Ribonucleic Acid Expressing Respiratory Syncytial Virus F Protein (RNA) (500 ng), lipid nanoparticle (LNP) alone, or LNPâformulated RNA (LNP_RNA). A single quadriceps from each mouse was homogenized using QIAzol reagent and the FastPrepâ24 instrument (MP Bio). Total RNA was purified using RNeasy columns according to the manufacturerâs instructions (Qiagen). RNA labeling, hybridization, and scanning were performed using methods, reagents, software, and hardware purchased from Agilent Technologies. Briefly, 100 ng RNA was retro transcribed, labeled using Cy3, and column purified Qiagen. The efficiency of Cy3 dye incorporation was assessed on a NanoDrop 1000 instrument. Reactions with specific activities >6 pmol dye/Î¼g cRNA were used for hybridization. cRNA (1.65 Î¼g) was hybridized onto a 4 X 44 Whole Mouse Genome Microarray (G4122F). After scanning, images were analyzed using Feature Extraction 10.7.3.1 software. Microarray data was analyzed using the R/Bioconductor Limma openâsource package. Briefly, each spot was background corrected and spot intensities between arrays normalized using the quantile method. The average normalized spot intensity from experimental replicates was determined and differentially expressed genes (compared to the PBS control group) calculated using a moderated tâstatistic (Empirical Bayes method) followed by BenjaminiâHochberg false discovery rate (FDR) correction. Genes with an FDR adjusted pâvalue â¤ 0.05 and a foldâchange greater than or less than 2 (log2 = 1) were considered significantly changed. Functional clustering was performed using the DAVID online database. Heat maps were generated using Spotfire 4.0.3 software.

Project description:BACKGROUND & AIM: Sessile serrated adenoma/polyps (SSA/Ps) are the likely culprit of ~20% colon cancers but they are molecularly poorly understood. We investigated their epigenetic phenotype using high-throughput analysis of DNA methylation and gene expression. METHODS: 17 SSA/Ps and, as a comparative group, 15 conventional adenomas (all with matched samples of normal mucosa) were prospectively collected during colonoscopy. DNA from the 64 tissues was analyzed, via bisulfite next generation sequencing, for methylation at ~2.7 million CpG sites located prevalently in gene regulatory regions spanning 80.5Mb (~2.5% of the genome). The transcriptome of these samples was also investigated using RNA sequencing. An independent series of 61 archival lesions was used for targeted verification of DNA methylation. RESULTS: Both SSA/Ps and conventional adenomas showed a profound remodelling of their methylome. Cytosine hypermethylation was more pervasive in SSA/Ps than adenomas, in terms of number of hypermethylated regions (22,147 vs 15,965, respectively) and genes (4938 vs 3443, respectively). In addition, the extent of hypermethylation in a given region was higher in SSA/Ps than adenomas. This methylation pattern of SSA/Ps was reminiscent of the CpG island methylator phenotype (CIMP) of their descendant cancers. We have called this phenotype proto-CIMP since most of the hypermethylation occurred in CpG islands and shores. SSA/Ps were also protected from a wave of demethylation that instead occurred in adenomas outside of CpG islands/shores (4288 vs 18,417 hypomethylated regions in SSAPs vs adenomas). Verification studies of six hypermethylated regions demonstrated the high potential of DNA methylation markers for predicting the diagnosis of SSA/Ps and/or adenomas. Proto-CIMP of SSA/Ps was surprisingly associated with a higher number of up- (618) than downregulated (349) genes, while adenomas showed the opposite trend (516 up- vs 712 downregulated genes). CONCLUSIONS: The epigenetic landscape of SSA/Ps differs substantially from that of conventional adenomas. This huge amount of epigenetic variation represents a rich source of promising diagnostic tools, such as novel DNA markers or histologic stainings, for the tailored management of the two most frequent colon cancer precursors.

Dataset Information

Transcription profiling of mouse muscle tissue after in-vivo intramuscularly administration of MF59, CpG, MF59+CpG, alum and PBS

Publications

Molecular and cellular signatures of human vaccine adjuvants.

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