|
| Status |
Public on Apr 04, 2017 |
| Title |
Transcriptomic Analysis of Endothelial Cells from Fibrovascular Membranes in Proliferative Diabetic Retinopathy |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: Identification of RUNX1 via next-generation sequencing (NGS) of fibrovascular membranes in patients with proliferative diabetic retinopathy.
Methods: Transcriptomic analysis with Illumina HiSeq2000 of fibrovascular membrane and control retina CD31+ samples. The sequence reads were analyzed with ANOVA (ANOVA) and targets with significance (fold change > +/-1.5 and p-value < 0.05) were selected for with Cufflinks, DeSeq2, Partek E/M, and EdgeR. qRT–PCR validation was performed using SYBR Green assays along with Western blots, siRNA, and MUSE proliferation assays.
Results: Using an optimized data analysis workflow, we mapped sequence reads per sample to the human genome (hg19) and identified genes that were statistically significant in all four statistical packages. P-values ranged from 8.78E-10 to 0.05. Using this gene list for ontology, highly significant annotation clusters included inflammatory, vascular development, and cell adhesion pathways.
Conclusions: Our study represents the first detailed transcriptomic analysis of CD31+ cells from fibrovascular membrane and CD31+ cells from control retinas with biologic replicates, generated by RNA-seq technology. The preferential selection of inflammatory and angiogenic pathways using this gene list is highly consistent with DR pathogenesis, which involves leaky and aberrant vessel growth.
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| Overall design |
CD31+ retinal mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
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| Contributor(s) |
Oh D, Lam J, D'Amore P, Kim L, Arboleda-Velasquez J |
| Citation(s) |
28400392 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R00 EY021624 |
Notch and TGF-beta in the Control of Retinal Vascular Integrity |
THE SCHEPENS EYE RESEARCH INSTITUTE, INC. |
Joseph Arboleda-Velasquez |
| UH2 NS100121 |
Exploring the Role of Aging in Cerebral Ischemic Small Vessel Disease Using Notch3 Mutant Mice |
THE SCHEPENS EYE RESEARCH INSTITUTE, INC. |
Joseph Arboleda-Velasquez |
| R01 EY005318 |
Cell-cell Interactions in the Retinal Vasculature |
THE SCHEPENS EYE RESEARCH INSTITUTE, INC. |
Patricia Ann D'Amore |
| R21 EY027061 |
Vasculogenesis in Thyroid Eye Disease |
THE SCHEPENS EYE RESEARCH INSTITUTE, INC. |
LEO A KIM |
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| |
| Submission date |
Jan 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph Arboleda-Velasquez |
| Organization name |
Schepens Eye Research Institute
|
| Street address |
20 Staniford St.
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (13)
|
| GSM2467182 |
fibrovascular membrane endothelial cells 2 |
| GSM2467183 |
fibrovascular membrane endothelial cells 3 |
| GSM2467184 |
fibrovascular membrane endothelial cells 4 |
| GSM2467185 |
fibrovascular membrane endothelial cells 5 |
| GSM2467186 |
fibrovascular membrane endothelial cells 6 |
| GSM2467187 |
fibrovascular membrane endothelial cells 7 |
| GSM2467188 |
fibrovascular membrane endothelial cells 8 |
| GSM2467189 |
fibrovascular membrane endothelial cells 9 |
| GSM2467190 |
Retinal endothelial cell sample 3 |
| GSM2467191 |
Retinal endothelial cell sample 4 |
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| Relations |
| BioProject |
PRJNA363068 |
| SRA |
SRP097696 |
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