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Comprehensive characterization of DNA methylation changes in Fuchs endothelial corneal dystrophy

View Article: PubMed Central - PubMed

ABSTRACT

Transparency of the human cornea is necessary for vision. Fuchs Endothelial Corneal Dystrophy (FECD) is a bilateral, heritable degeneration of the corneal endothelium, and a leading indication for corneal transplantation in developed countries. While the early onset, and rarer, form of FECD has been linked to COL8A2 mutations, the more common, late onset form of FECD has genetic mutations linked to only a minority of cases. Epigenetic modifications that occur in FECD are unknown. Here, we report on and compare the DNA methylation landscape of normal human corneal endothelial (CE) tissue and CE from FECD patients using the Illumina Infinium HumanMethylation450 (HM450) DNA methylation array. We show that DNA methylation profiles are distinct between control and FECD samples. Differentially methylated probes (10,961) were identified in the FECD samples compared with the control samples, with the majority of probes being hypermethylated in the FECD samples. Genes containing differentially methylated sites were disproportionately annotated to ontological categories involving cytoskeletal organization, ion transport, hematopoetic cell differentiation, and cellular metabolism. Our results suggest that altered DNA methylation patterns may contribute to loss of corneal transparency in FECD through a global accumulation of sporadic DNA methylation changes in genes critical to basic CE biological processes.

No MeSH data available.


Gene Ontology (GO) categories most strongly enriched among probes in FECD CE.Number of represented probes in each category is in parentheses after category name. (A) Gene body DNA hypomethylation, (B) Gene body DNA hypermethylation, (C) Promoter DNA hypomethylation, and (D) Promoter DNA hypermethylation.
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pone.0175112.g004: Gene Ontology (GO) categories most strongly enriched among probes in FECD CE.Number of represented probes in each category is in parentheses after category name. (A) Gene body DNA hypomethylation, (B) Gene body DNA hypermethylation, (C) Promoter DNA hypomethylation, and (D) Promoter DNA hypermethylation.

Mentions: In general, DNA methylation changes did not closely correlate with individual pathways. The most strongly enriched ontologies among differentially methylated promoter and gene body regions were categories containing few genes assayed by a small number of probes, suggesting a high false positive rate and that no pathways show consistent DNA methylation in FECD. However, among the subset of enriched categories that contained large numbers of genes, many correspond to biological functions necessary for the unique functions of the corneal endothelium. Specifically, gene body DNA hypomethylation was disproportionately present in genes involved in fluid and ion transport in the FECD samples, the largest category being Transport (p = 0.0376) (Fig 4A). This result is consistent with prior studies that have found reduced expression of gene families associated with ion and water transport in the CE of FECD patients including bicarbonate transporter-related protein-1 (BTR1) [35], aquaporin-1 (AQP1) [36], and monocarboxylate transporters (MCTs) [37]. By contrast, gene body DNA hypermethylation was associated with hematopoetic cell differentiation in the FECD samples, especially related to Immune System Processes (p = 0.0065) (Fig 4B). Promoter DNA hypomethylation in the FECD samples also showed enrichment of gene families related to cytoskeletal organization, such as Microtubule Anchoring (p = 0.0229) and Microtubule Depolymerization (p = 0.0213) (Fig 4C). Proper expression of cytoskeletal factors is necessary for the function of CE to restrict fluid leakage into the corneal stroma [3]. Promoter DNA hypermethylation was observed in gene families involved in metabolic processes, including Reactive Oxygen Species Metabolic Processes (p = 0.012) and Phosphorus Metabolic Processes (p = 0.027) (Fig 4D). This result correlates with the prior finding that mitochondrial transcripts are depleted in FECD [35].


Comprehensive characterization of DNA methylation changes in Fuchs endothelial corneal dystrophy
Gene Ontology (GO) categories most strongly enriched among probes in FECD CE.Number of represented probes in each category is in parentheses after category name. (A) Gene body DNA hypomethylation, (B) Gene body DNA hypermethylation, (C) Promoter DNA hypomethylation, and (D) Promoter DNA hypermethylation.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5383226&req=5

pone.0175112.g004: Gene Ontology (GO) categories most strongly enriched among probes in FECD CE.Number of represented probes in each category is in parentheses after category name. (A) Gene body DNA hypomethylation, (B) Gene body DNA hypermethylation, (C) Promoter DNA hypomethylation, and (D) Promoter DNA hypermethylation.
Mentions: In general, DNA methylation changes did not closely correlate with individual pathways. The most strongly enriched ontologies among differentially methylated promoter and gene body regions were categories containing few genes assayed by a small number of probes, suggesting a high false positive rate and that no pathways show consistent DNA methylation in FECD. However, among the subset of enriched categories that contained large numbers of genes, many correspond to biological functions necessary for the unique functions of the corneal endothelium. Specifically, gene body DNA hypomethylation was disproportionately present in genes involved in fluid and ion transport in the FECD samples, the largest category being Transport (p = 0.0376) (Fig 4A). This result is consistent with prior studies that have found reduced expression of gene families associated with ion and water transport in the CE of FECD patients including bicarbonate transporter-related protein-1 (BTR1) [35], aquaporin-1 (AQP1) [36], and monocarboxylate transporters (MCTs) [37]. By contrast, gene body DNA hypermethylation was associated with hematopoetic cell differentiation in the FECD samples, especially related to Immune System Processes (p = 0.0065) (Fig 4B). Promoter DNA hypomethylation in the FECD samples also showed enrichment of gene families related to cytoskeletal organization, such as Microtubule Anchoring (p = 0.0229) and Microtubule Depolymerization (p = 0.0213) (Fig 4C). Proper expression of cytoskeletal factors is necessary for the function of CE to restrict fluid leakage into the corneal stroma [3]. Promoter DNA hypermethylation was observed in gene families involved in metabolic processes, including Reactive Oxygen Species Metabolic Processes (p = 0.012) and Phosphorus Metabolic Processes (p = 0.027) (Fig 4D). This result correlates with the prior finding that mitochondrial transcripts are depleted in FECD [35].

View Article: PubMed Central - PubMed

ABSTRACT

Transparency of the human cornea is necessary for vision. Fuchs Endothelial Corneal Dystrophy (FECD) is a bilateral, heritable degeneration of the corneal endothelium, and a leading indication for corneal transplantation in developed countries. While the early onset, and rarer, form of FECD has been linked to COL8A2 mutations, the more common, late onset form of FECD has genetic mutations linked to only a minority of cases. Epigenetic modifications that occur in FECD are unknown. Here, we report on and compare the DNA methylation landscape of normal human corneal endothelial (CE) tissue and CE from FECD patients using the Illumina Infinium HumanMethylation450 (HM450) DNA methylation array. We show that DNA methylation profiles are distinct between control and FECD samples. Differentially methylated probes (10,961) were identified in the FECD samples compared with the control samples, with the majority of probes being hypermethylated in the FECD samples. Genes containing differentially methylated sites were disproportionately annotated to ontological categories involving cytoskeletal organization, ion transport, hematopoetic cell differentiation, and cellular metabolism. Our results suggest that altered DNA methylation patterns may contribute to loss of corneal transparency in FECD through a global accumulation of sporadic DNA methylation changes in genes critical to basic CE biological processes.

No MeSH data available.