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Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement

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Published on: January 19, 2017

Tissue-specific TCF4 triplet repeat instability revealed by optical genome mapping.

Christina Zarouchlioti¹, Stephanie Efthymiou², Stefano Facchini²

¹UCL Institute of Ophthalmology, London, UK.

|September 15, 2024

Summary

Fuchs endothelial corneal dystrophy (FECD) is linked to TCF4 repeat expansions. Optical genome mapping reveals extreme CTG18.1 instability in diseased corneal cells, offering new therapeutic targets for FECD and similar repeat-mediated diseases.

Keywords:

Fuchs endothelial corneal dystrophy Optical genome mapping Somatic mosaicism Tissue-specific repeat instability Trinucleotide repeat expansion disease Triplet repeat expansion-mediated disease

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Published on: February 3, 2013

Area of Science:

Genomics
Ophthalmology
Molecular Biology

Background:

Fuchs endothelial corneal dystrophy (FECD) is a common human repeat-mediated disease.
It affects corneal endothelial cells (CECs) and is often linked to TCF4 intronic triplet repeats (CTG18.1).
Understanding the tissue-specific instability of these repeats is crucial for FECD pathophysiology.

Purpose of the Study:

To investigate the tissue-specific instability of the CTG18.1 repeat in FECD using optical genome mapping (OGM).
To gain mechanistic insights into how CTG18.1 instability contributes to FECD.
To explore the potential of OGM as a tool for analyzing repeat instability in disease.

Main Methods:

Applied OGM to genomic DNA from FECD patients and controls (n=43), including CECs, leukocytes, and fibroblasts.
Developed a bioinformatics pipeline to analyze CTG18.1-spanning DNA molecules.
Compared OGM results with conventional polymerase chain reaction-based fragment analysis.

Main Results:

Expanded CTG18.1 alleles showed dynamic behavior across different cell types.
Clusters of CTG18.1 molecules (approx. 1800-11,900 repeats) were exclusively found in diseased CECs from expansion-positive FECD cases.
Progenitor allele size and patient age influenced leukocyte-specific CTG18.1 instability.

Conclusions:

OGM is a powerful tool for analyzing somatic instability of repeat loci.
Extreme CTG18.1 instability in diseased CECs is a key factor in FECD pathophysiology.
These findings suggest new therapeutic avenues for FECD and other diseases caused by somatically unstable repeats.