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| Status |
Public on Nov 18, 2020 |
| Title |
Gene-regulatory network analysis of ankylosing spondylitis with a single-cell chromatin accessible assay |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
A detailed understanding of the gene-regulatory network in ankylosing spondylitis (AS) is vital for elucidating the mechanisms of AS pathogenesis. Assaying transposase-accessible chromatin in single cell sequencing (scATAC-seq) is a suitable method for revealing such networks. Thus, scATAC-seq was applied to define the landscape of active regulatory DNA in AS. As a result, there was a significant change in the percent of CD8+ T cells in PBMCs, and 37 differentially accessible transcription factor (TF) motifs were identified. T cells, monocytes-1 and dendritic cells were found to be crucial for the IL-17 signaling pathway and TNF signaling pathway, since they had 73 potential target genes regulated by 8 TF motifs with decreased accessibility in AS. Moreover, natural killer cells were involved in AS by increasing the accessibility to TF motifs TEAD1 and JUN to induce cytokine-cytokine receptor interactions. In addition, CD4+ T cells and CD8+ T cells may be vital for altering host immune functions through increasing the accessibility of TF motifs NR1H4 and OLIG (OLIGI and OLIG2), respectively. These results explain clear gene regulatory variation in PBMCs from AS patients, providing a foundational framework for the study of personal regulomes and delivering insights into epigenetic therapy.
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| Overall design |
Single-cell chromatin accessibility (scATAC) profiles of human peripheral blood mononuclear cells in ankylosing spondylitis
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| Contributor(s) |
Yu H, Wu H, Dai Y |
| Citation(s) |
33173081, 34880858 |
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| Submission date |
Sep 07, 2020 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Haiyan YU |
| E-mail(s) |
[email protected]
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| Organization name |
Shenzhen People's Hospital
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| Street address |
No. 1017, North of Dongmen Road
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| City |
Shenzhen |
| ZIP/Postal code |
518020 |
| Country |
China |
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| Platforms (1) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA662087 |
| SRA |
SRP280364 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE157595_RAW.tar |
56.9 Mb |
(http)(custom) |
TAR (of BED, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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