|
| Status |
Public on Aug 28, 2023 |
| Title |
Experimental upregulation of developmentally downregulated ribosomal protein large subunits 7 and 7A promotes axon regeneration after injury in vivo [scRNA-Seq] |
| Sample organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
Ribosomal proteins are involved in neurodevelopment and central nervous system (CNS) disease and injury. However, the roles of specific ribosomal protein subunits in developmental axon growth, and their potential as therapeutic targets for treating CNS injuries, are still poorly understood. Here, we show that ribosomal protein large (Rpl) and small (Rps) subunit genes are substantially (56-fold) enriched amongst the genes, which are downregulated during maturation of retinal ganglion cell (RGC) CNS projection neuron. We also show that RGC subtype-specific Rpl and Rps subunits are highly co-regulated, and partially re-upregulated after optic nerve crush (ONC). Because developmental downregulation of ribosomal proteins coincides with developmental decline in neuronal intrinsic axon growth capacity, we hypothesized that Rpl/Rps incomplete re-upregulation after injury may be a part of the cellular response which attempts to reactivate intrinsic axon growth mechanism. We found that experimentally upregulating Rpl7 and Rpl7A promoted axon regeneration after ONC in vivo. Finally, we characterized gene networks associated with Rpl/Rps, and showed that Rpl7 and Rpl7A belong to the cluster of genes, which are shared between translational and neurodevelopmental biological processes (based on gene-ontology) that are co-downregulated in maturing RGC during the decline in intrinsic axon growth capacity.
|
| |
|
| Overall design |
Normalized matrices and cell metadata (e.g., type assignment) for embryonic, adult uninjured, and adult injured RGCs, are available from the GEO accession numbers GSE122466 and GSE137400. Postnatal RGC scRNA-seq dataset we previously generated is available under the Gene Expression Omnibus (GEO) accession number GSE115404.
Cell-counts matrices were obtained from the GEO submissions from the previously published data. Matrices were loaded as seurat objects in R.
Seurat objects were merged and expression was normalized. A cell counts matrix for the merged dataset was then generating by extracting counts matrix from seurat object.
The condition each cell belongs to was appended to the cell ID in the columns of the matrix
mm10
One CSV files: Containg RGC embyonic, postnatal, adult and injured cells' normalized expression values for each gene.
|
| Web link |
https://www.sciencedirect.com/science/article/pii/S0014488623001954?via%3Dihub
|
| |
|
| Contributor(s) |
Theune WC, Jian X, Trakhtenberg EF |
| Citation(s) |
37633482 |
| |
| Submission date |
Aug 07, 2023 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Ephraim F Trakhtenberg |
| E-mail(s) |
trakhtenberg@uchc.edu
|
| Organization name |
University of Connecticut School of Medicine
|
| Department |
Neuroscience
|
| Street address |
263 Farmington Ave. RM L4005
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030 |
| Country |
USA |
| |
|
| This SubSeries is part of SuperSeries: |
| GSE240317 |
Experimental upregulation of developmentally downregulated ribosomal protein large subunits 7 and 7A promotes axon regeneration after injury in vivo |
|
| Relations |
| Reanalysis of |
GSM4148508 |
| Reanalysis of |
GSM3466902 |
| Reanalysis of |
GSM3466903 |
| Reanalysis of |
GSM3177677 |
| Reanalysis of |
GSM3177678 |
| Reanalysis of |
GSM3907320 |
| Reanalysis of |
GSM3907321 |
| Reanalysis of |
GSM3907322 |
| Reanalysis of |
GSM3907323 |
| Reanalysis of |
GSM3907324 |
| Reanalysis of |
GSM3907325 |
| Reanalysis of |
GSM3907326 |
| Reanalysis of |
GSM3907327 |
| Reanalysis of |
GSM3907328 |
| Reanalysis of |
GSM3907329 |
| Reanalysis of |
GSM4078555 |
| Reanalysis of |
GSM4078556 |
| Reanalysis of |
GSM4078557 |
| Reanalysis of |
GSM4078558 |
