 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 12, 2023 |
| Title |
DNA methylation dynamics during esophageal epithelial regeneration following repair with acellular silk fibroin grafts in rat |
| Organism |
Rattus norvegicus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Bi-layer silk fibroin (BLSF) scaffolds represent an emerging technology in the development of acellular biomaterials for esophageal repair. Their therapeutic potential is attributed to their robust mechanical properties, elasticity, and low immunogenicity. However, the underlying molecular mechanisms of scaffold-mediated wound healing processes in the esophagus remain unclear. Previous research has identified signaling cascades involved in neoepithelial regeneration in a rat model of onlay esophagoplasty with BLSF grafts, including c-MET, TrkA, and PI3K-Akt signaling. Interestingly, these pro-survival signaling cascades are largely governed by DNA methylation (DNAme). Such findings motivate us to apply reduced-representation bisulfite sequencing (RRBS) to characterize the temporal dynamics of DNAme in host and regenerated tissues up to 1 week post-operation. Globally, we observe hypermethylation at post-surgical repair timepoints and an inverse correlation between DNAme and the expression levels of differentially expressed proteins during regeneration. Site-specific hypomethylation targets genes associated with immune activation, which may be indicative of immune cell infiltration at the surgical implant site, while site-specific hypermethylation appears to target PI3K-Akt signaling. Our work provides mechanistic insight into the molecular processes governing esophageal regeneration, which can motivate therapeutic innovations toward temporal modulation of tissue regeneration during scaffold-mediated esophageal repair via epigenetic regulators that target key pathways.
|
| |
|
| Overall design |
Reduced-representation bisulfite sequencing (RRBS) with rat esophageal tissues in nonsurgical controls (NSC, n=4), and 1 day (n=5) or 1 week (n=5) after surgical repair with Bi-layer silk fibroin (BLSF) scaffolds.
|
| Web link |
https://doi.org/10.1002/adbi.202200160
|
| |
|
| Contributor(s) |
Gundogdu G, Shao H, Mauney J, Downing TL, Urban LA, Trinh A, Li J, Nguyen T |
| Citation(s) |
36658732 |
| Submission date |
May 14, 2022 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Timothy Downing |
| E-mail(s) |
tim.downing@uci.edu
|
| Organization name |
UCI
|
| Department |
Department of Biomedical Engineering
|
| Lab |
Downing Lab
|
| Street address |
419 S. Circle View Drive
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
|
| Samples (14)
|
|
| Relations |
| BioProject |
PRJNA838203 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE203028_RAW.tar |
206.2 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...