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| Status |
Public on May 07, 2024 |
| Title |
lncRNA CDKN2B-AS1 regulates collagen expression |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The long noncoding RNA CDKN2B-AS1 harbors a major coronary artery disease risk haplotype, which is also associated with progressive forms of the oral inflammatory disease periodontitis as well as myocardial infarction (MI). Despite extensive research, there is currently no broad consensus on the function of CDKN2B-AS1 that would explain a common molecular role of this lncRNA in these diseases. Our aim was to investigate the role of CDKN2B-AS1 in gingival cells to better understand the molecular mechanisms underlying the increased risk of progressive periodontitis. We downregulated CDKN2B-AS1 transcript levels in primary gingival fibroblasts with LNA GapmeRs. Following RNA-sequencing, we performed differential expression, gene set enrichment analyses and Western Blotting. Putative causal alleles were searched by analyzing associated DNA sequence variants for changes of predicted transcription factor binding sites. We functionally characterized putative functional alleles using luciferase-reporter and antibody electrophoretic mobility shift assays in gingival fibroblasts and HeLa cells. Of all gene sets analysed, collagen biosynthesis was most significantly upregulated (Padj=9.7x10-5 (AUC>0.65) with the CAD and MI risk gene COL4A1 showing strongest upregulation of the enriched gene sets (Fold change = 12.13, Padj = 4.9 x 10-25). The inflammatory "TNFA signaling via NFKB" gene set was downregulated the most (Padj=1x10-5 (AUC=0.60). On the single gene level, CAPNS2, involved in extracellular matrix organization, was the top upregulated protein coding gene (Fold change=48.5, P<9x10-24). The risk variant rs10757278 altered a binding site of the pathogen responsive transcription factor STAT1 (P=5.8x10-6). rs10757278-G allele reduced STAT1 binding 14.4% and rs10757278-A decreased luciferase activity in gingival fibroblasts 41.2% (P=0.0056), corresponding with GTEx data. CDKN2B-AS1 represses collagen gene expression in gingival fibroblasts. Dysregulated collagen biosynthesis through allele-specific CDKN2B-AS1 expression in response to inflammatory factors may affect collagen synthesis, and in consequence tissue barrier and atherosclerotic plaque stability.
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| Overall design |
To establish the molecular function of the lncRNA CDKN2B-AS1, we downregulated CDKN2B-AS1 transcript levels in cultures of primary gingival fibroblasts from 3 different donors with LNA GapmeRs. We then performed gene expression profiling by RNA-Sequencing with RNA extracted 48 hours after LNA GapmeR transfection. 3 control samples were transfected with negative control GapmeRs and matched with the 3 samples that were transfected with LNA GapmeRs that targeted CDKN2B-AS1. Additionally, we transfected an immortalized (hTERT) human gingival fibroblast cell line (ihGF; Applied Biological Materials Inc, cat.-no T0026) with LNA GapmeRs that targeted CDKN2B-AS1 and with negative control LNA GapmeRs
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Authors state "no file provided due to donor privacy concerns".
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| Contributor(s) |
Shi W, Song J, Chopra A, Weiner JM, Dommisch H, Beule D, Schaefer AS |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 02, 2024 |
| Last update date |
May 07, 2024 |
| Contact name |
January 3rd Weiner |
| E-mail(s) |
january.weiner@gmail.com
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| Phone |
030450543049
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| Organization name |
Berlin Institute of Health, Charité Medical University of Berlin
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| Department |
CUBI
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| Street address |
Charitéplatz 1
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| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (8)
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| GSM8247934 |
Homo sapiens oral mucosa gingivial fibroblasts, negative control GapmeRs, donor pFB2, replicate N1 |
| GSM8247935 |
Homo sapiens oral mucosa gingivial fibroblasts, LNA GapmeRs targeting the lncRNA CDKN2B-AS1, donor pFB2, replicate M2 |
| GSM8247936 |
Homo sapiens oral mucosa gingivial fibroblasts, negative control GapmeRs, donor pFB3, replicate N1 |
| GSM8247937 |
Homo sapiens oral mucosa gingivial fibroblasts, LNA GapmeRs targeting the lncRNA CDKN2B-AS1, donor pFB3, replicate M1 |
| GSM8247938 |
Homo sapiens oral mucosa gingivial fibroblasts, negative control GapmeRs, donor pFB39, replicate N2 |
| GSM8247939 |
Homo sapiens oral mucosa gingivial fibroblasts, LNA GapmeRs targeting the lncRNA CDKN2B-AS1, donor pFB39, replicate M2 |
| GSM8247940 |
Homo sapiens oral mucosa gingivial fibroblasts, negative control GapmeRs, donor IHGF, replicate N2 |
| GSM8247941 |
Homo sapiens oral mucosa gingivial fibroblasts, LNA GapmeRs targeting the lncRNA CDKN2B-AS1, donor IHGF, replicate M2 |
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| Relations |
| BioProject |
PRJNA1107262 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE266478_raw_counts.tsv.gz |
738.3 Kb |
(ftp)(http) |
TSV |
| Raw data not provided for this record |
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