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Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine peripheral blood mononuclear cells (PBMCs) [RNA-Seq]

ABSTRACT: We report the application of RNA sequencing technology for high-throughput profiling of the aluminium hydroxide adjuvant mechanism of action in an in vivo experiment on sheep. We mapped about 52 million sequence reads per sample to the sheep genome (build Oar3.1) and identified 21,274 genes in the PBMCs of sheep treated with commercial vaccines or with the adjuvant alone. A total of 2473, 2980 and 429 differentialy expressed genes were identified in the vaccine tf VS vaccine t0, adjuvant tf VS adjuvant t0 and adjuvant tf VS vaccine tf comparisons, respectively. Previously reported genes related to alterations caused by aluminium adjuvant were found differentially expressed, namely: NLRP3, IL1B, IL8, TNF, NFKB2, RELA and RELB. In addition, most of the genes related to apoptosis were up-regulated in both group after treatment. In contrast, other genes related to immune response, inflammatory response and cell-cell signalling were up-regulated in Vac-injected sheep and whereas down-regulated in Adj-injected animals. Taken together, our analysis provides characterization of alterations in the transcriptome caused by the aluminium adjuvant and identifies increased expression of inflammatory cytokines, NF-KB family genes and apoptotic genes.

ORGANISM(S): Ovis aries

PROVIDER: GSE113898 | GEO | 2018/10/30

REPOSITORIES: GEO

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Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine peripheral blood mononuclear cells (PBMCs) [miRNA-Seq]

Project description:We report the application of miRNA sequencing technology for high-throughput profiling of the aluminium hydroxide adjuvant mechanism of action in an in vivo experiment on sheep. We mapped about 13 million sequence reads per sample to the sheep genome (build Oar3.1) and identified 95 miRNAs in the PBMCs of sheep treated with commercial vaccines or with the adjuvant alone. A total of 3, 6 and 1 differentialy expressed miRNAs were identified in the vaccine tf VS vaccine t0, adjuvant tf VS adjuvant t0 and adjuvant tf VS vaccine tf comparisons, respectively. Furthermore, miRNA target prediction was performed and it was integrated with previous RNA-seq data in the same animals to predict reliable miRNA-mRNA interactions. Previously reported miRNAs related to alterations caused by aluminium adjuvant were found differentially expressed, namely: miR-19b and miR-125b. Within the negatively correlated targets of the differentially expressed miRNAs there are factors that are clearly related with the response to stimulus, RNA binding and cellular response to DNA damage. Taken together, our analysis provides characterization of alterations in the miRNAome caused by the aluminium adjuvant and identifies some targets of the differentially expressed miRNAs which have been previously linked to the immune system. The overrepresentation of genes related to DNA damage stimulus and DNA repair in both groups may be due to miRNA-mediated regulation.

2018-10-30 | GSE113897 | GEO

Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine encephalon. [RNA-Seq]

Project description:We report the application of RNA sequencing technology for high-throughput profiling of the aluminium hydroxide adjuvant mechanism of action in an in vivo experiment on sheep treated with commercial vaccines, with the adjuvant alone or with PBS (control group). We mapped about 74.1 million sequence reads per sample to the sheep genome (build Oar3.1) and after filtering 16,369 genes were expressed, of which 14,387 were annotated genes in Ensembl and 1,982 were candidate lncRNAs. A total of 13, 63 and 76 differentialy expressed genes were identified in the Vaccine vs. Control, Adjuvant vs. Control and Adjuvant vs. Vaccine comparisons, respectively. Previously reported genes related to neuronal development, brain transport and neurotransmission, brain injury and neurodegenerative diseases associated with aluminum were found differentially expressed, namely VCAM1, TRPM4, GDF10 and NTN1.

2020-10-02 | GSE128595 | GEO

Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine encephalon. [miRNA-Seq]

Project description:We report the application of miRNA sequencing technology for high-throughput profiling of the aluminium hydroxide adjuvant mechanism of action in an in vivo experiment on sheep. We mapped about 13.1 million sequence reads per sample to the sheep genome (build Oar3.1) and identified 299 miRNAs in the encephalon of sheep treated with commercial vaccines, with the adjuvant alone or with PBS (control group). A total of 2, 38 and 7 differentialy expressed miRNAs were identified in the Vaccine vs. Control, Adjuvant vs. Control and Adjuvant vs. Vaccine comparisons, respectively. Furthermore, miRNA target prediction was performed and it was integrated with previous RNA-seq data in the same animals to predict reliable miRNA-mRNA interactions. Previously reported miRNAs related to brain injury and neurodegenerative diseases were found differentially expressed. Within the negatively correlated targets of the differentially expressed miRNAs there are factors that are clearly related with mitochondria, to maintenance of neuronal polarity and axon growth and to apoptosis. Taken together, our analysis provides characterization of alterations in the miRNAome caused by the aluminium adjuvant alone, while the commercial vaccine not cause great changes, and identifies some targets of the differentially expressed miRNAs which have been previously linked to mitochondrial dysfunction. Aluminum might be causing an imbalance in metal ion levels, among them Mg, in the parietal lobe cortex of animals vaccinated with the adjuvant alone.

2020-10-02 | GSE128596 | GEO

Identification and characterization of miRNAs in spleens of sheep subjected to repetitive vaccination

Project description:Spleen miRNA profiles of twelve age-matched Rasa sheep after inoculation of nine different commercial vaccines based of aluminium hydroxide (the vaccine group composed of 4 animals), with the aluminium adjuvant alone in an equivalent dose (the adjuvant group composed of 4 animals) or PBS (the control group composed of 5 animals) were generated by deep sequencing on an Illumina HiSeq2500 sequencer.

2023-05-12 | GSE180596 | GEO

Analysis of transcriptome response of rhizobia to aluminium toxicity

Project description:Purpose: High throughput sequencing has revolutionized methods of microbial pathway analysis in response to various envoronmental stimuli. The aim of this study was to determine mechanisms in which Rhizobium phaseoli employ towards tolerance or resistance to aluminium toxicity through RNA sequencing. Methods: Total RNA was extracted from bacteria treated with aluminium after 48 hours with trizol and sequenced with illumina’s Miseq at Novogene Corporation Inc. U.K. After QC, reads were aligned to the genome with bowtie2 and differential expression performed with DESeq2. Results: Sequencing resulted to about 6.7-9.0 M reads that aligned to all the four plasmids and one chromosome of R. phaseoli genome. Most enriched genes were found localized in the membrane of the bacteria. Conclusion: The membrane of R. phaseoli is possibly the target site for toxicity and tolerance against aluminium toxicity. This is the first time such a study is described.

2022-01-17 | GSE193556 | GEO

Exploring the molecular mechanisms of positive and negative regulation of apoptosis post Orf virus infection in sheep

Project description:Contagious ecthyma (Orf) is a contagious disease with worldwide distribution, caused by the epitheliotropic Orf virus (ORFV), a member of the genus Parapoxvirus. In the current study, we collected the oral mucosa tissues samples (T0, T3, T7 and T15) from sheep at 0, 3, 7 and 15 days post ORFV infection, respectively. To explore the changes of comprehensive transcriptome of host cells from oral mucosa tissues post ORFV infection, the RNA-seq transcriptome comparisons were performed on these samples. It showed that 1928, 3219 and 2646 differentially expressed genes (DEGs) were identified among T3 vs. T0, T7 vs. T0, T15 vs. T0 respectively. Through Gene Ontology (GO) analyses of the DEGs from these comparisons, it revealed that ORFV provoked the vigorous immune response of the host cells during the early stage of infection. Moreover, GO and network analysis revealed that positive and negative regulative mechanisms of apoptosis worked as whole in the host cells, in order to reach a homeostasis of oral mucosa tissues.

2018-02-13 | GSE95203 | GEO

Transcriptome analysis of total blood cells from sheep after vaccination with FMDV vaccines

Project description:Transcriptome analysis of total blood cells from sheep collected at 0, 4 and 24 hours after vaccination with inactivated FMDV vaccine, and adenovirus (human Ad5)-based vaccines encoding FMDV antigens, with and without Montanide ISA206 VG adjuvant.

2019-12-10 | GSE135609 | GEO

mRNA profiling of NMuMG mouse mammary epithelial cells incubated for 4 weeks in the presence of aluminium chloride vs controls incubated in parallel in the presence of the same dilution of solvent (H2O) alone

Project description:Salts of aluminium, a chemical element devoid of biological function, are added to many industrial products of frequent use because of aluminium's chemical versatility. As a result of lifetime exposure, aluminium accumulates in several organs including the mammary gland. At concentrations in the range of those measured in the breast of women living in industrialised countries, aluminium chloride transforms human and mouse mammary epithelial cells in vitro. These results challenge the safety commonly ascribed to aluminium and suggest that it could be a human carcinogen. NMuMG is a spontaneously immortalised, non tumorigenic mouse mammary epithelial cell line originally derived from NAMRU mice that, following chronic culture in the presence of aluminium - in the form of AlCl3 x 6H2O - becomes able to form tumors and metastasis in NOD-scid and nude mice. As a part of our investigations on the mechanisms by which aluminium might transform mammary epithelial cells, we analysed the mRNA profile of NMuMG cells incubated for 4 weeks - a time duration that precedes cellular transformation - in the presence of aluminium or the corresponding untreated controls cultured in parallel, by cDNA microarray. We used the Clariom S microarray from Thermofisher, that covers more than 20'000 well annotated mRNAs.

2020-11-30 | E-MTAB-9764 | biostudies-arrayexpress

mRNA profiling of HC11 mouse mammary epithelial cells incubated for 4 weeks in the presence of aluminium chloride vs controls incubated in parallel in the presence of the same dilution of solvent (H2O) alone

Project description:Salts of aluminium, a chemical element devoid of biological function, are added to many industrial products of frequent use because of aluminium's chemical versatility. As a result of lifetime exposure, aluminium accumulates in several organs including the mammary gland. At concentrations in the range of those measured in the breast of women living in industrialised countries, aluminium chloride transforms human and mouse mammary epithelial cells in vitro. These results challenge the safety commonly ascribed to aluminium and suggest that it could be a human carcinogen. HC11 is a spontaneously immortalised, non tumorigenic mouse mammary epithelial cell line originally derived from Balb/c mice that, following chronic culture in the presence of aluminium - in the form of AlCl3 x 6H2O - becomes able to form tumors and metastasis in the immunocompetent and immunocompatible strain Balb/cByJ. As a part of our investigations on the mechanisms by which aluminium might transform mammary epithelial cells, we analysed the mRNA profile of HC11 cells incubated for 4 weeks - a time duration that precedes cellular transformation - in the presence of aluminium or the corresponding untreated controls cultured in parallel, by cDNA microarray. We used the Clariom S microarray from Thermofisher, that covers more than 20'000 well annotated mRNAs.

2020-11-30 | E-MTAB-9763 | biostudies-arrayexpress

mRNA profiling of HC11 mouse mammary epithelial cells transformed in vitro by long-term incubation in the presence of aluminium chloride vs controls incubated in parallel in the presence of the same dilution of solvent (H2O) alone.

Project description:Salts of aluminium, a chemical element devoid of biological function, are added to many industrial products of frequent use because of aluminium's chemical versatility. As a result of lifetime exposure, aluminium accumulates in several organs including the mammary gland. At concentrations in the range of those measured in the breast of women living in industrialised countries, aluminium chloride transforms human and mouse mammary epithelial cells in vitro. These results challenge the safety commonly ascribed to aluminium and suggest that it could be a human carcinogen. HC11 is a spontaneously immortalised, non tumorigenic mouse mammary epithelial cell line originally derived from Balb/c mice that, following chronic culture in the presence of aluminium - in the form of AlCl3 x 6H2O - becomes able to form tumors and metastasis in the immunocompetent and immunocompatible strain Balb/cByJ. As a part of our investigations on the mechanisms by which aluminium might transform mammary epithelial cells, we analysed the mRNA profile of HC11 cells transformed in vitro by aluminium or the corresponding untreated controls cultured in parallel by cDNA microarray. We used the Clariom S microarray from Thermofisher, that covers more than 20'000 well annotated mRNAs.

2020-11-30 | E-MTAB-9723 | biostudies-arrayexpress

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