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Decoding the m6A expression profiling of spinal cord after spared nerve injury at three time points with RIP-Seq

ABSTRACT: We performed gene expression profiling analysis using data obtained from RNA-seq and m6A peaks profiling analysis using data obtained from RIP-Seq of spared nerve injury model at 3rd, 7th, 14th postoperative day and sham group. To investigate the differential m6A expression profiling, we established spared nerve injury model at 3rd, 7th, 14th postoperative day and sham group.

ORGANISM(S): Mus musculus

PROVIDER: GSE202166 | GEO | 2022/05/06

REPOSITORIES: GEO

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Small extracellular vesicles from spared nerve injury model and sham control mice differentially regulate gene expression in primary microglia

Project description:Nerve injury outcomes might be predicted by examining small extracellular vesicles (sEVs) in circulation, as their biomolecular cargo facilitates cellular communication and can alter transcriptional state and behavior of recipient cells. We found that sEVs from the serum of spared nerve injury (SNI) model male mice had seven differentially expressed miRNAs compared to sEVs from sham-operated control mice four weeks post-surgery. We investigated how these sEVs alter transcription in primary cortical microglia, a crucial mediator of neuropathic pain, using RNA sequencing. While the uptake of sEVs from both SNI model and sham groups changed gene expression in microglia compared to PBS treatment, sEVs from the sham group induced a more drastic change, particularly in genes involved in immune response. This was recapitulated by increased levels of pro-inflammatory cytokines and chemokines in microglia incubated with sEVs from sham control compared to sEVs from SNI model, naïve mice, or PBS. However, treating microglia with sEVs from female mice showed that serum sEVs derived from female SNI mice but not from female sham mice induced a more pronounced microglial secretion of pro-inflammatory mediators. Our data demonstrate that the molecular changes induced by sham surgery injuring skin and muscles are reflected in circulating sEVs in male mice four weeks later. Thus, when using sEVs from sham mice as control in comparative mechanistic studies after nerve injury, sex of mice should be taken into consideration.

2023-06-27 | GSE228065 | GEO

rat T Cells: Sham vs. SNI

Project description:DNA methylation profiles of T cells comparing 9 months post Spared Nerve Injury (SNI) rats with Sham rats.

2015-10-01 | GSE70007 | GEO

rat PFC: Sham vs. SNI

Project description:DNA methylation profiles of prefrontal cortec (PFC) comparing 9 months post Spared Nerve Injury (SNI) rats with Sham rats.

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Desipramine Induces Anti-inflammatory Dorsal Root Ganglion Transcriptional Signatures in the Murine Spared Nerve Injury Model

Project description:Monoamine-targeting antidepressants serve as frontline medications for chronic pain and associated comorbidities. While persistent anti-allodynic properties of antidepressants generally require weeks of treatment, several groups have demonstrated acute analgesic effects within hours of administration, suggesting a role in non-mesocorticolimbic pain processing regions such as the peripheral nervous system. To further explore this possibility, after four weeks of spared nerve injury or sham surgeries, we systemically administered desipramine or saline for an additional three weeks and performed whole transcriptome RNA sequencing on injured dorsal root ganglia. Along with alterations in molecular pathways associated with neuronal activity, we observed a robust immunomodulatory transcriptional signature in the desipramine treated group. Cell subtype deconvolution predicted that these changes were associated with A- and C-fibers. Of note, differentially expressed genes from the dorsal root ganglia of DMI-treated, injured mice were largely unique compared to those from the nucleus accumbens of the same animals. These observations suggest that, under peripheral nerve injury conditions, desipramine induces specific gene expression changes across various regions of the nociceptive circuitry.

2024-04-03 | GSE261676 | GEO

Decoding the m6A expression profiling of spinal cord after spared nerve injury at three time points with RIP-Seq

Project description:Decoding the m6A expression profiling of spinal cord after spared nerve injury at three time points with RIP-Seq

| PRJNA834826 | ENA

Transcriptome changes in the dorsal root ganglion (DRG) after spared nerve injury (SNI) in adult and infant rats.

Project description:To investigate differences in response to nerve injury between adult and infant rats, adult and infant rats underwent SNI or sham surgery.

2023-08-31 | GSE237869 | GEO

Single cell RNA sequencing analysis of mouse dorsal root ganglions (DRGs) with and without spared nerve injury.

Project description:We report here a systematic approach to characterize the transcriptional responses of different cells types in the dorsal root ganglion (DRG) to peripheral nerve injury using single cell RNA sequencing (scRNAseq). We compare scRNAseq datasets of lumbar DRGs form naïve mice with corresponding datasets from mice subjected to spared nerve injury (SNI) 7 or 14 days prior to analysis. SNI surgery was performed in the left and right hindleg and development of mechanical allodynia was monitored by von Frey testing relative to control mice and the baseline level. Mice were perfused with PBS prior to extraction of L3 and L4 DRGs and DRGs were enzymatically and mechanically dissociated to single cell suspension before scRNAseq. Analysis of transcriptional changes in this nerve injury-paradigm reveals a differential response at 7 days versus 14 days post injury, suggesting dynamic gene modulation over time.

2021-09-01 | GSE174430 | GEO

rattus

Project description:spared nerve injury model of rattus comapred with sham control Raw sequence reads

| PRJNA384664 | ENA

Single-nucleus analysis of intact spinal cord and spared tissue after complete injury in rhesus monkey

Project description:The lumbar spinal cord is fundamental for hindlimb function and serves as spared tissue after spinal cord injury (SCI). However, our knowledge about cellular heterogeneity of the intact spinal cord and spared tissues is still scarce especially in primates. Here, we used single-nucleus RNA sequencing analysis in rhesus monkey to characterize the cellular heterogeneity of the spinal cord and profile the dynamic changes of cells in spared tissues after complete thoracic SCI. We found that rhesus monkey and mice shared a highly conserved pattern of cellular constitution but with divergent gene expression. After SCI, the cellular characteristics of spared tissue changed permanently and showed a regionally diverse response. We identified an emerging oligodendrocyte subtype that responded to interferon and a new permanently activated microglia subtype that was responsible for eliminating cell debris. Overall, our findings revealed dynamic changes of cells in spared tissue, providing comprehensive insights for SCI repair.

2023-07-26 | GSE199669 | GEO

Comparative proteomics analysis of Brassica napus in response to drought stress

Project description:Drought is one of the most severe stresses leading to retardation of plant growth and development and loss of crop yield. Here we examined the proteome changes of an important oil seed crop canola Brassica napus under drought stress over a 14 day period. Using iTRAQ LC-MS/MS, we identified 2,244 proteins expressed during drought stress. Among them, 412 proteins showed significant changes in abundance under stress, and 67, 243, 287, and 79 proteins were differentially expressed in 3rd, 7th, 10th, and 14th day of drought stress, respectively. Functional analysis of the 412 proteins indicated that the number of proteins associated with “Metabolism”, “Protein synthesis”, and “Signaling” decreased, while those related to “Photosynthesis” and “Stress and defense” increased in response to drought stress. In particular, the proteome profiles at the 7th and 10th day were similar to each other, although there were much more post-translational modifications (PTM) at the 10th day of drought. Interestingly, 286 of 2,244 proteins exhibited PTMs in response to drought stress, 82 of which were differentially changed in drought-stressed plants, and 60 were observed at the 10th day. Furthermore, comparison of protein expression changes with those of gene transcription showed that there was positive correlation in B. napus, although there were different patterns between transcripts and proteins at each time point. As drought stress prolongs, most of the protein abundance changes may be attributed to gene transcription, and PTMs clearly contribute to the protein diversity and functions.

2016-07-06 | PXD001409 | Pride

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