Transcriptome analysis of the human corneal endothelium - PubMed (original) (raw)

Transcriptome analysis of the human corneal endothelium

Ricardo F Frausto et al. Invest Ophthalmol Vis Sci. 2014.

Abstract

Purpose: To comprehensively characterize human corneal endothelial cell (HCEnC) gene expression and age-dependent differential gene expression and to identify expressed genes mapped to chromosomal loci associated with the corneal endothelial dystrophies posterior polymorphous corneal dystrophy (PPCD)1, Fuchs endothelial corneal dystrophy (FECD)4, and X-linked endothelial dystrophy (XECD).

Methods: Total RNA was isolated from ex vivo corneal endothelium obtained from six pediatric and five adult donor corneas. Complementary DNA was hybridized to the Affymetrix GeneChip 1.1ST array. Data analysis was performed using Partek Genomics Suite software, and differentially expressed genes were validated by digital molecular barcoding technology.

Results: Transcripts corresponding to 12,596 genes were identified in HCEnC. Nine genes displayed the most significant differential expression between pediatric and adult HCEnC: CAPN6, HIST1H3A, HIST1H4E, and HSPA2 were expressed at higher levels in pediatric HCEnC, while ITGBL1, NALCN, PREX2, TAC1, and TMOD1 were expressed at higher levels in adult HCEnC. Analysis of the PPCD1, FECD4 and XECD loci demonstrated transcription of 53/95 protein-coding genes in the PPCD1 locus, 27/40 in the FECD4 locus, and 35/68 in the XECD locus.

Conclusions: An analysis of the HCEnC transcriptome reveals the expression of almost 13,000 genes, with less than 1% mapped to chromosomal loci associated with PPCD1, FECD4, and XECD. At least nine genes demonstrated significant differential expression between pediatric and adult HCEnC, defining specific functional properties distinct to each age group. These data will serve as a resource for vision scientists investigating HCEnC gene expression and can be used to focus the search for the genetic basis of the corneal endothelial dystrophies for which the genetic basis remains unknown.

Keywords: HCEnC; corneal endothelial dystrophy; corneal endothelium; gene expression; transcriptome.

Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

PubMed Disclaimer

Figures

Figure 1

Figure 1

Principal component analysis and hierarchical clustering of ex vivo HCEnC gene expression data sets. (A) PCA demonstrated three distinct groupings, with the adolescent (17 and 18 years, red spheres) HCEnC group having a closer relationship to adult samples (53–70 years, blue spheres) compared to preadolescents (10 and 11 years, green spheres) and preschoolers (4 and 6 years, violet spheres). (B) Hierarchical clustering confirmed the relationships observed with PCA, with the adolescent HCEnC samples (red bars) demonstrating a closer relationship to adult HCEnC samples (blue bars). (C) After removal of the HCEnC samples from the adolescent group, PCA demonstrated three distinct groupings, two of which were analyzed together as the pediatric group (preschooler and preadolescent, 4–11 years, blue spheres) and the adult group (53–57 years, red spheres). Subsequent data analysis was performed on two groups defined by the colored ovals (pediatric and adult). (D) Hierarchical clustering confirmed the relationships observed in the PCA analysis, with the preschooler (violet bar) and the preadolescent (green bar) HCEnC samples having clustered separately from the adult (blue bar) HCEnC.

Figure 2

Figure 2

Hierarchical clustering analysis was performed for genes that demonstrated significant (non-FDR P value = 0.05, FC > 2) differential expression between pediatric (preschooler and preadolescent) and adult endothelium.

Figure 3

Figure 3

Differentially expressed genes were validated by digital molecular barcoding technology. The fold change (FC) for each gene was greater than 2. Transcript levels for the TAC1, PREX2, ITGBL1, TMOD1, and NALCN genes were higher in adult samples (black bars), while transcript levels for the HIST1H3A, HISTH4E, HSPA2, and CAPN6 genes were higher in pediatric samples (white bars). (*P < 0.05, ***P < 0.001).

References

    1. Krafchak CM, Pawar H, Moroi SE, et al. Mutations in TCF8 cause posterior polymorphous corneal dystrophy and ectopic expression of COL4A3 by corneal endothelial cells. Am J Hum Genet. 2005; 77: 694–708. - PMC - PubMed
    1. Aldave AJ, Yellore VS, Yu F, et al. Posterior polymorphous corneal dystrophy is associated with TCF8 gene mutations and abdominal hernia. Am J Med Genet A. 2007; 143A: 2549–2556. - PubMed
    1. Liskova P, Tuft SJ, Gwilliam R, et al. Novel mutations in the ZEB1 gene identified in Czech and British patients with posterior polymorphous corneal dystrophy. Hum Mutat. 2007; 28: 638. - PMC - PubMed
    1. Vincent AL, Niederer RL, Richards A, Karolyi B, Patel DV, McGhee CN. Phenotypic characterisation and ZEB1 mutational analysis in posterior polymorphous corneal dystrophy in a New Zealand population. Mol Vis. 2009; 15: 2544–2553. - PMC - PubMed
    1. Nguyen DQ, Hosseini M, Billingsley G, Heon E, Churchill AJ. Clinical phenotype of posterior polymorphous corneal dystrophy in a family with a novel ZEB1 mutation. Acta Ophthalmol. 2010; 88: 695–699. - PubMed

Publication types

MeSH terms

Substances

Supplementary concepts

LinkOut - more resources