Transcriptomic Responses of Human Retinal Vascular Endothelial Cells to Inflammatory Cytokines

Feargal J. Ryan, Yuefang Ma, Liam M. Ashander, Michael Kvopka, Binoy Appukuttan, David J. Lynn, Justine R. Smith

Research output: Contribution to journalArticlepeer-review

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Abstract

Purpose: Molecular profiling of human retinal endothelial cells provides opportuni-ties to understand the roles of this cell population in maintenance of the blood-ocular barrier, and its involvements in diverse retinal vasculopathies. We aimed to generate a transcriptome of human retinal endothelial cells in the unstimulated state, and following treatment with inflammatory cytokines linked to cell dysfunction. 

Methods: Endothelial cells were isolated from retinae of five human cadaveric donors, and treated for 60 minutes and 24 hours with interleukin-1β or tumor necrosis factor-α, or exposed to medium alone for the same intervals. Expression of intercellular adhesion molecule-1 was measured by RT-qPCR to confirm cytokine-induced activation of the cells. RNA was sequenced on the Illumina NovaSeq 6000 platform. Reads were aligned to the human GRCh38 genome, and reads that aligned to Ensembl-annotated genes were counted. Quality control of sequencing was performed with FastQC, and sequences were classified by Kraken. 

Results: A human retinal endothelial cell RNA-sequencing dataset with mean of 99% reads aligned to the human genome was produced as raw RNA sequence data (FASTQ files) and processed read data (XLSX files). Multidimensional scaling analysis showed a strong donor effect, which was readily controlled by ComBat. 

Conclusions: Our dataset may be useful for human retinal endothelial cell transcrip-tomic assemblies, functional gene annotating and/or gene expression and enrichment analyses, as well as cross-dataset harmonization. 

Translational Relevance: The molecular profile of the human retinal endothelium is a source of candidate biologic targets for retinal vasculopathies.

Original languageEnglish
Article number27
Number of pages9
JournalTranslational Vision Science and Technology
Volume11
Issue number8
DOIs
Publication statusPublished - Aug 2022

Keywords

  • cytokine
  • endothelial
  • human
  • retinal
  • transcriptome

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