Transcriptomic analysis of organotypic porcine retina cultures
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Abstract
Porcine organotypic retinal explant cultures are widely used to study retinal neurodegeneration under controlled conditions, but the biological process that occurs in the retinal explant over time due to preparation-induced injury and culture are not well understood. Here, we generated a time-resolved transcriptomic reference for porcine neural retinal explants-maintained ex vivo for 10 days. Global expression profiles are strongly separated by culture time, with Day 0 clearly distinct from cultured samples and at Day 7 and Day 10 showing the highest similarity, indicating a transition toward a later stabilized state. Across the time course, 3,187 genes were differentially expressed relative to Day 0, with the largest shifts occurring at an early stage of culture (Day 1–Day 3). Pathway-level analyses revealed coordinated remodeling involving inflammatory signaling, and metabolic/bioenergetic changes, including reduced mitochondrial and oxidative phosphorylation–related programs at later time points. Here, we provide a time-resolved transcriptomics reference dataset for cultured porcine retinal explants. These data can build a foundation to interpret data generated in this model, differentiate changes inherent to the explant culture from treatment-specific effects and to select appropriate experimental windows for mechanistic studies of retinal degeneration.
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Abstract
Porcine organotypic retinal explant cultures are widely used to study retinal neurodegeneration under controlled conditions, but the biological process that occurs in the retinal explant over time due to preparation-induced injury and culture are not well understood. Here, we generated a time-resolved transcriptomic reference for porcine neural retinal explants-maintained ex vivo for 10 days. Global expression profiles are strongly separated by culture time, with Day 0 clearly distinct from cultured samples and at Day 7 and Day 10 showing the highest similarity, indicating a transition toward a later stabilized state. Across the time course, 3,187 genes were differentially expressed relative to Day 0, with the largest shifts occurring at an early stage of culture (Day 1–Day 3). Pathway-level analyses revealed coordinated remodeling involving inflammatory signaling, and metabolic/bioenergetic changes, including reduced mitochondrial and oxidative phosphorylation–related programs at later time points. Here, we provide a time-resolved transcriptomics reference dataset for cultured porcine retinal explants. These data can build a foundation to interpret data generated in this model, differentiate changes inherent to the explant culture from treatment-specific effects and to select appropriate experimental windows for mechanistic studies of retinal degeneration.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Siavash Khos- ravi{at}gmail.com, grazia.giorgio{at}boehringeringelheim.com, federica.staurenghi{at}boehringer-ingelheim.com, tanja.schoenberger{at}boehringer-ingelheim.com, peter.gross{at}boehringeringelheim.com, margit.ried{at}boehringeringelheim.com, julia.frankenhauser{at}boehringer-ingelheim.com, sebastian.eder{at}boehringer-ingelheim.com, elke.markert{at}boehringeringelheim.com, remko.bakker{at}boehringeringelheim.com, sepideh.babaei{at}boehringer-ingelheim.com, nina.zippel{at}boehringeringelheim.com
Abbreviations
- AMD
- age-related macular degeneration
- B-27
- B-27 supplement
- BH
- Benjamini–Hochberg (multiple-testing correction
- BP
- biological process
- bp
- base pairs
- CO2
- carbon dioxide
- DESeq2
- DESeq2 (R/Bioconductor package for RNA-seq differential expression
- DGE
- differential gene expression
- DR
- diabetic retinopathy
- ECM
- extracellular matrix
- FDR
- false discovery rate
- GEO
- Gene Expression Omnibus
- GFAP
- Glial fibrillary acidic protein
- GO
- Gene Ontology
- GO-BP
- Gene Ontology Biological Process
- GO-
- Gene Ontology Slim (high-level GO subset
- Slim
- GSEA
- gene set enrichment analysis
- GSVA
- gene set variation analysis
- Iba1
- ionized calcium-binding adapter molecule 1
- log2FC
- log2 fold change
- LOX-1
- lectin-like oxidized low-density lipoprotein receptor 1
- mRNA
- messenger RNA
- NaCl
- sodium chloride
- NES
- normalized enrichment score
- NF-κB
- nuclear factor kappa B
- ONC
- optic nerve crush
- PCA
- principal component analysis
- RGC
- retinal ganglion cell
- RIN
- RNA integrity number
- RLT
- RLT lysis buffer (Qiagen
- RNA
- ribonucleic acid
- RNA-
- RNA sequencing
- seq
- RPE
- retinal pigment epithelium
- VST
- variance-stabilizing transformation
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- last seen: 2026-05-20T01:45:00.602351+00:00
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- last seen: 2026-05-22T02:00:06.705733+00:00
License: CC-BY-NC-4.0