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Gene expression in response to axotomy in organotypical slices co-cultures

ABSTRACT: Brain slice cultures offer advantages over other in vitro methods, as they mimic numerous in vivo aspects. For most purposes, slices of the developing brain, termed organotypic slice cultures , preserve a high degree of cellular differentiation and tissue organization. The entorhino-hippocampal connection (EHP) is the main entrance of information to the hippocampus proper and the dentate gyrus. Also it has some specific features that make them particularly interesting in studies of axonal regeneration: (i) the culture method obviates the need for extensive animal surgery and requires less time than other in vivo approaches; (ii) the EHP is reproduced easily in vitro in cultures with a degree of laminar specificity similar to that found in vivo; (iii) the EHP is myelinated both in vitro and in vivo; and (iv) most of the cellular and molecular barriers to axon regeneration are present after the axotomy of the EHP in vitro. Altogether this model is useful to evaluate axon regeneration and putative estrategies to promote axonal growth. Keywords: organotypic slice cultures; axonal lession; gene expression

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE20528 | GEO | 2011/02/25

SECONDARY ACCESSION(S): PRJNA125143

REPOSITORIES: GEO

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Gene expression in response to axotomy in organotypical slices co-cultures

Project description:Brain slice cultures offer advantages over other in vitro methods, as they mimic numerous in vivo aspects. For most purposes, slices of the developing brain, termed organotypic slice cultures , preserve a high degree of cellular differentiation and tissue organization. The entorhino-hippocampal connection (EHP) is the main entrance of information to the hippocampus proper and the dentate gyrus. Also it has some specific features that make them particularly interesting in studies of axonal regeneration: (i) the culture method obviates the need for extensive animal surgery and requires less time than other in vivo approaches; (ii) the EHP is reproduced easily in vitro in cultures with a degree of laminar specificity similar to that found in vivo; (iii) the EHP is myelinated both in vitro and in vivo; and (iv) most of the cellular and molecular barriers to axon regeneration are present after the axotomy of the EHP in vitro. Altogether this model is useful to evaluate axon regeneration and putative estrategies to promote axonal growth. Keywords: organotypic slice cultures; axonal lession; gene expression To evaluate the genes whose transcription was regulated after 1, 3 and 7 days after EHP (Entorhino-Hippocampal Pathway) axotomy, RNA samples were analyzed with Agilent whole genome rat long oligonucleotide (44 K base) probe based microarrays.

2011-02-25 | E-GEOD-20528 | biostudies-arrayexpress

Prostate cancer organotypic slice cultures (OSC) treated with E2 or DHT

Project description:Organotypic slice cultures from prostate cancer patients were generated and treated with or without 17b-estradiol or DHT to study estrogen and androgen signalling pathways.

2020-10-06 | GSE142287 | GEO

Prostate cancer organotypic slice cultures (OSC) treated with E2 or DHT

Project description:Prostate cancer organotypic slice cultures (OSC) treated with E2 or DHT

| PRJNA596471 | ENA

Activating injury-responsive genes with hypoxia enhances axon regeneration through neuronal HIF-1α

Project description:Injured peripheral neurons successfully activate a pro-regenerative transcriptional program to enable axon regeneration and functional recovery. How transcriptional regulators coordinate the expression of such programs remains unclear. Here we show that hypoxia-inducible factor 1α (HIF-1α) controls multiple injury-induced genes in sensory neurons and contribute to the pre-conditioning lesion effect. Knockdown of HIF-1α in vitro or conditional knockout in vivo impairs sensory axon regeneration. The HIF-1α target gene Vascular Endothelial Growth Factor A (VEGFA) is expressed in injured neurons and contributes to stimulate axon regeneration. Induction of HIF-1α using hypoxia enhances axon regeneration in vitro and in vivo in sensory neurons. Hypoxia also stimulates motor neuron regeneration and accelerates neuromuscular junction reinnervation. This study demonstrates that HIF-1α represents a critical transcriptional regulator in regenerating neurons and suggests hypoxia as a tool to stimulate axon regeneration.

2016-01-21 | GSE73415 | GEO

RNA-sequencing of injured cultured dorsal root ganglion neurons over time

Project description:Injured sensory neurons activate a transcriptional program necessary for robust axon regeneration and eventual target reinnervation. Understanding the transcriptional regulators that govern this axon regenerative response may guide therapeutic strategies to promote axon regeneration in the injured nervous system. Here, we used cultured dorsal root ganglia neurons to identify pro-regenerative transcription factors. Using RNA sequencing, we first characterized this neuronal culture and determined that embryonic day 13.5 DRG (eDRG) neurons cultured for 7 days are similar to e15.5 DRG neurons in vivo and that all neuronal subtypes are represented. This eDRG neuronal culture does not contain other non-neuronal cell types. Next, we performed RNA sequencing at different time points after in vitro axotomy. Analysis of differentially expressed genes revealed upregulation of know regeneration associated transcription factors, including Jun Atf3 and Rest, paralleling the axon injury response in vivo. Analysis of transcription factor binding sites in differentially expressed genes revealed other known transcription factors promoting axon regeneration, such as Myc, Hif1a, Pparg, Ascl1a, Srf, as well as other transcription factors not yet characterized in axon regeneration. We next tested if overexpression of known and novel candidate transcription factors alone or in combination promote axon regeneration in vitro. Our results demonstrate that expression of Ctcf with Yy1 or E2f2 enhances in vitro axon regeneration. Our analysis reveals that pairs of transcription factors can functionally synergize to promote axon regeneration and highlight that transcription factor interaction play an important role as a regulator of axon regeneration.

2022-06-20 | GSE138480 | GEO

Anti-Nogo-A antibody treatment of Rat Hippocampal Slice Cultures

Project description:The neurite outgrowth inhibitory myelin protein Nogo-A has been well studied in the context of central nervous system (CNS) injury and disease. We studied the effects of the application of neutralizing anti-Nogo-A antibodies (11C7 and 7B12) in intact CNS tissue in vitro using rat organotypic hippocampal slice cultures. This study had the purpose of elucidating the role of Nogo-A in the adult intact CNS and determining the consequences of its neutralization through antibody application. In vitro cultures treated with anti-Nogo-A antibody showed an elicited growth response. The results also gave indications that hippocampal circuitry might be altered due to the regulation at the synaptic and neurotransmission level.

2008-11-12 | GSE12483 | GEO

Dietary restriction of cysteine and methionine sensitizes gliomas to ferroptosis and induces alterations in energetic metabolism

Project description:Ferroptosis is mediated by lipid peroxidation of phospholipids containing polyunsaturated fatty acyl moieties. Glutathione, the key cellular antioxidant capable of inhibiting lipid peroxidation via the activity of the enzyme glutathione peroxidase 4 (GPX-4), is generated directly from the sulfur-containing amino acid cysteine, and indirectly from methionine via the transsulfuration pathway. Herein we show that cysteine and methionine deprivation (CMD) can synergize with the GPX4 inhibitor RSL3 to increase ferroptotic cell death and lipid peroxidation in both murine and human glioma cell lines and in ex vivo organotypic slice cultures. We also show that a cysteine-depleted, methionine-restricted diet can improve therapeutic response to RSL3 and prolong survival in a syngeneic orthotopic murine glioma model. Finally, this CMD diet leads to profound in vivo metabolomic, proteomic and lipidomic alterations, highlighting the potential for improving the efficacy of ferroptotic therapies in glioma treatment with a non-invasive dietary modification.

2023-01-11 | MTBLS5959 | MetaboLights

Transcription profiling of Xenopus dorsal root ganglia conditioned in vitro vs freshly dissected control

Project description:Axonal regeneration is enhanced by prior conditioning peripheral nerve lesions. Here we show that Xenopus dorsal root ganglia (DRGs) with attached peripheral nerves (PN-DRGs) can be conditioned in vitro, thereafter showing enhanced axonal growth in response to neurotrophins, similar to preparations conditioned by axotomy in vivo. In contrast to freshly dissected preparations, conditioned PN-DRGs show abundant neurotrophin-induced axonal growth in the presence of actinomycin D, suggesting synthesis of mRNA encoding proteins necessary for axonal elongation occurs during the conditioning period, and this was confirmed by oligonucleotide micro-array analysis.

2008-04-16 | E-MEXP-1297 | biostudies-arrayexpress

Experimental gene expression of developmentally downregulated Crmp1, Crmp4, and Crmp5 promotes axon regeneration and retinal ganglion cell survival after optic nerve injury [third-party re-analysis]

Project description:Collapsin response mediator proteins (Crmps) play roles in neuronal development and axon growth. However, neuronal-specific roles of Crmp1, Crmp4, and Crmp5 in regeneration of injured central nervous system (CNS) axons in vivo are unclear. Here, we analyzed developmental and subtype-specific expression of Crmp genes in retinal ganglion cells (RGCs), tested whether overexpressing Crmp1, Crmp4, or Crmp5 in RGCs through localized intralocular AAV2 delivery promotes axon regeneration after optic nerve injury in vivo, and characterized developmental co-regulation of gene-concept networks associated with Crmps. We found that all Crmp genes are developmentally downregulated in RGCs during maturation. However, while Crmp1, Crmp2, and Crmp4 were expressed to a varying degree in most RGC subtypes, Crmp3 and Crmp5 were expressed only in a small subset of RGC subtypes. We then found that after optic nerve injury, Crmp1, Crmp4, and Crmp5 promote RGC axon regeneration to varying extents, with Crmp4 promoting the most axon regeneration and also localizing to axons. We also found that Crmp1 and Crmp4, but not Crmp5, promote RGC survival. Finally, we found that Crmp1, Crmp2, Crmp4, and Crmp5's ability to promote axon regeneration is associated with neurodevelopmental mechanisms, which control RGC’s intrinsic axon growth capacity.

2023-04-10 | GSE228486 | GEO

Experimental gene expression of developmentally downregulated Crmp1, Crmp4, and Crmp5 promotes axon regeneration and retinal ganglion cell survival after optic nerve injury [bulk RNA-seq]

2023-04-10 | GSE228485 | GEO

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