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Accession: PRJNA499078 ID: 499078

Transcriptomic and gene ontology profiling of the human corneal cell types (human)

See Genome Information for Homo sapiens
Purpose: To identify distinct gene expression and functional profiles for the three main cell types (epithelial, keratocyte and endothelial) of the human cornea. Methods: RNA-sequencing was performed using total RNA isolated from ex vivo corneal epithelial cells (evCEpC), keratocytes (evK) and endothelial cells (evCEnC) obtained from 3 donor corneas obtained from a commercial eye bank. Transcriptomic analysis was performed using Kallisto (alignment (hg38) and quantification) and Sleuth (differential gene expression(DGE)), with transcript abundances calculated as transcripts per kilobase million (TPM). Expression was defined as TPM≥7.5 and significant DGE as a fold-change ≥4 and a false-discovery rate adjusted p-value≤0.05. Cell type specificity was defined as genes adhering to the above expression and DGE criteria and not expressed (i.e., TPM<7.5) in the other two cell types. Gene ontology enrichment analysis was performed on the cell type-specific gene lists using the gene group functional profiling (g:GOSt) tool within the web-based g:Profiler suite. Results: We identified 205 genes specific in evCEpC, and enrichment of epithelial-associated GO terms (e.g., cornified envelope, epidermis development, cell-cell adhesion). We identified 76 genes specific in evK, and fibroblast-associated GO terms (e.g., collagen metabolic process, metallopeptidase activity, extracellular matrix organization). We identified 96 genes specific in evCEnC, and at least one CEnC-associated GO term (e.g., cellular cation homeostasis) but several synapse-associated GO terms (e.g., synapse organization, synapse part). Conclusions: The human cornea is comprised of three main cell types that play important roles in maintaining corneal clarity and vision. Our results demonstrate that a small subset (0.4-1%) of the protein-coding genes confers distinct and classic functional properties associated with each cell type. In addition, we identified a novel association and significant functional overlap between CEnC and synapses. This may lead to insights into the molecular mechanisms of transendothelial transport and secretion, which are integral metabolic features of the corneal endothelium. Overall design: Corneal epithelium, corneal endothelium and corneal stroma were isolated from three donor corneas (i.e., 3 biological replicates). Keratocyte RNA was isolated from corneal stroma tissue.
AccessionPRJNA499078; GEO: GSE121922
Data TypeTranscriptome or Gene expression
ScopeMultiisolate
OrganismHomo sapiens[Taxonomy ID: 9606]
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo; Homo sapiens
Publications (total 3)
  • Frausto RF et al., "Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion.", Sci Rep, 2020 May 4;10(1):7402
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Grants
  • "Identification and Characterization of the Genetic Basis of PPCD" (Grant ID R01 EY022082, National Eye Institute)
SubmissionRegistration date: 29-Oct-2018
Cornea Genetics Laboratory, Ophthalmology, Stein Eye Institute, UCLA
RelevanceMedical
Project Data:
Resource NameNumber
of Links
Sequence data
SRA Experiments9
Publications
PubMed3
PMC3
Other datasets
BioSample9
GEO DataSets1
GEO Data Details
ParameterValue
Data volume, Supplementary Mbytes1
SRA Data Details
ParameterValue
Data volume, Gbases8
Data volume, Mbytes3184

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