Omics · study · 2026
Characterization of cellular responses of Ptpn6 (SHP-1) cKO in hippocampus by scRNA-seq
Listed in NCBI GEO
Ptpn6 (SHP-1) is known to impact signaling pathways in immune cells in various different ways, and in many cases, SHP1 opposes immune cell activation by nonreceptor tyrosine kinases such as Syk, Jak or ZAP70.
Description
In Alzheimer’s disease, multiple AD risk genes are expressed in microglia and related to microglial regulation and function. SHP-1 interacts with ITIM domains of multiple AD GWAS genes including Siglec-11, LILRB2, PILRA, and CD33 and SHP-1 is also known as a negative regulator of DAP12/Trem2 signaling.
To understand cellular pathways of ITIM signaling and delineate benefits and liabilities of ITIM signaling inhibition, here we characterize Ptpn6 cKO (Cohort I) and Ptpn6 cKO crossed with previously characterized AD mouse model TauPS2APP (Cohort II) by single cell RNA-seq. We found that Ptpn6 deletion unleashes disease-like transcriptional changes in vivo. We also discovered distinct microglia activation states associated with protective versus exacerbative Ptpn6 genotypes.
Read the rest (1 more)
Current scRNA-seq results reveal both protective and latent degenerative potential of microglia held in check by Ptpn6.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE312nnn/GSE312503 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE312503 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1374068 ncbi.nlm.nih.gov/bioproject/PRJNA1374068 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Mus musculus
- From keywords
- Life Sciences
- Inferred from text
- Disease 75% · RNA sequencing 65% · Single-cell RNA sequencing 65%
Provenance · 1 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE312503 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:disease | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:single-cell-rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[organism].NCBITaxon:10090 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |