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| Status |
Public on Jan 18, 2020 |
| Title |
Transcriptional signatures that define Ulcerative Colitis in remission |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Background: This study addresses whether existing specific transcriptional profiles can improve and support the current status of the definition of ulcerative colitis (UC) remission apart from the existing endoscopic, histologic, and laboratory scoring systems. For that purpose, a well-stratified UC patient population in remission was compared to active UC and control patients and was investigated by applying the next-generation technology RNA-Seq.
Methods: Mucosal biopsies from patients in remission (n = 14), patients with active UC (n = 14), and healthy control patients (n = 16) underwent whole-transcriptome RNA-Seq. Principal component analysis, cell deconvolution methods, gene profile enrichment, and pathway enrichment methods were applied to define a specific transcriptional signature of UC in remission.
Results: Analyses revealed specific transcriptional signatures for UC in remission with increased expression of genes involved in O-glycosylation (MUC17, MUC3A, MUC5AC, MUC12, SPON1, B3GNT3), ephrin-mediated repulsion of cells (EFNB2E, EFNA3, EPHA10, EPHA1), GAP junction trafficking (TUBA1C, TUBA4A, TUBB4B, GJB3, CLTB), and decreased expression of several toll-like receptors (TLR1, TLR3, TLR5, TLR6).
Conclusions: This study reveals specific transcriptional signatures for remission. Partial restoration and improvement of homeostasis in the epithelial mucus layer and revival of immunological functions were observed. A clear role for bacterial gut flora composition can be implied. The results can be useful for the development of treatment strategies for UC in remission and may be useful targets for further investigations aiming to predict the outcome of UC in the future.
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| Overall design |
Mucosal biopsies from UC patients in remission (n=14), UC patients (n=14), and healthy controls (n=16) underwent RNA-Seq. Principal component analyse (PCA), cell deconvolution methods and diverse statistical methods were applied to obtain and characterize a dataset of significantly differentially expressed gens (DEGs) during UC remission.
** Raw data not provided due to patient privacy concerns. **
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| Contributor(s) |
Paulssen RH, Fenton C |
| Citation(s) |
32322884, 37199828, 38514698 |
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| Submission date |
Mar 21, 2019 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Christopher Fenton |
| E-mail(s) |
[email protected]
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| Phone |
4748196479
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| Organization name |
Universiry of Tromso
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| Department |
GSCT
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| Street address |
MH bygget
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| City |
Tromso |
| State/province |
Norge |
| ZIP/Postal code |
9037 |
| Country |
Norway |
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| Platforms (1) |
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| Samples (44)
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| Relations |
| BioProject |
PRJNA528490 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE128682_DESeq2_normalized_counts.tab.gz |
1.5 Mb |
(ftp)(http) |
TAB |
| GSE128682_RAW.tar |
8.2 Mb |
(http)(custom) |
TAR (of TAB) |
| GSE128682_raw_counts.tab.gz |
1.5 Mb |
(ftp)(http) |
TAB |
| GSE128682_readMe.txt |
361 b |
(ftp)(http) |
TXT |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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