Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of cuprizone mouse model following AAV-mediated delivery of A Proliferation Inducing Ligand

ABSTRACT: A Proliferation Inducing Ligand (APRIL) is a member of the tumour necrosis factor (TNF) superfamily and has recently been shown to modulate pro-inflammatory astrocyte responses, as well as to ameliorate disease outcome in the experimental autoimmune encephalomyelitis mouse model for multiple sclerosis (MS). We demonstrated that adeno-associated virus (AAV)-mediated delivery of APRIL was able to rescue immune-stimulated murine iPSC-derived neurospheroids from detrimental cell death and neurodegenerative processes. In addition, T2 and diffusion weighted MRI with histological confirmation demonstrated that AAV-mediated secretion of APRIL by cortical neurons could reduce cuprizone-induced neuro-inflammation and/or demyelination in the splenium of the corpus callosum. To further document the beneficial effect of APRIL, a transcriptome-proteome integration study for the splenium was performed that revealed the activation of cellular pathways associated with alternative immune cell polarisation, cell survival and neuroregeneration. Here, the associated transcriptome data (FASTQ files and BAM files) are deposited.

INSTRUMENT(S): Not applicable, Element AVITI, Qubit 4.0 and TapeStation

ORGANISM(S): Mus musculus

SUBMITTER: Steven Van Laere

PROVIDER: E-MTAB-14516 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The organic acids lactate and diacetate are commonly used in combination in ready-to-eat foods because they show synergistic, i.e. greater than additive, ability to inhibit the growth of Listeria monocytogenes. Full genome microarrays were used to investigate the synergistic transcriptomic response of two L. monocytogenes strains, h7858 (serotype 4b) and f6854 (serotype 1/2a), to organic acid, under conditions controlling for osmotic and cold stress. Strains were exposed to BHI broth at 7°C with 4.65% water phase (w.p.) NaCl at pH 6.1 treated with 2% w.p. potassium lactate, 0.14% w.p. sodium diacetate, the combination of both at the same levels, or no inhibitors as control. RNA was extracted 8h after exposure, during lag phase, to capture gene expression changes during adaptation to the organic acid stress. Treatment with organic acids induced massive global transcriptional changes, with 1041 and 640 genes differentially expressed in h7858 and f6854. Major effects of treatment with lactate and diacetate are (i) a total of 474 and 209 genes, for h7858 and f6854, that showed synergistic expression differences, (ii) differential expression of membrane ion transport genes including those encoding ABC transporters of metals and decreased multi-drug transporter expression many ABC, PTS, and drug transporter systems, including increased PTS sugar transport and decreased multi-drug transporter expression, and (iii) altered metabolism including induction of a nutrient limiting stress response, reduction of menaquinone biosynthesis, and a shift from fermentative production of lactate and acetate and lactate to energetically less favorable, neutral acetoin. These data suggest that additional synergies in L. monocytogenes growth inhibition could be achieved by treatments that interfere with cellular energy generation processes. The dye-swapped, single loop design hybridizes a single biological replicate of both 2% water phase lactate (PL) and 0.14% water phase acetate (SDA) treatments to both the control (CTRL) and combination (PLSDA) treatments (4 hybridizations), using opposite dye labels for each sample, and a second biological replicate is hybridized with dye assignments swapped (4 more hybridizations) to balance labeling effects. The design was repeated twice comprising 16 hybridizations over 4 biological replicates for each strain, and 32 total hybridizations over both h7858 and f6854.

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Transcriptome analysis of cuprizone mouse model following AAV-mediated delivery of A Proliferation Inducing Ligand

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