January 17, 2023 -- Tel Aviv University researchers have discovered new clues to the causes of adult-onset macular degeneration (AMD). By combining a map of gene regulatory sites with disease-associated loci, they uncovered new genetic AMD risk factors. The study, published January 17 in the journal PLOS Biology, may advance the understanding of AMD, a leading cause of blindness in adults.
AMD results from dysfunction in the retinal pigmented epithelium (RPE), a layer of tissue sandwiched between the photoreceptors that receive light, and the choriocapillaris, which nourishes the retina. The researchers began by exploring a transcription factor (a protein that regulates specific genes) called LHX2, which is central to RPE development. Using RPE derived from human stem cells, they suppressed LHX2 activity and found that most affected genes were downregulated (producing fewer cellular components), indicating that LHX2 serves as a transcriptional activator binding to regulatory sites on the genome to increase other genes' activity.
They also found that one affected gene, called OTX2, collaborated with LHX2 to regulate many genes in the RPE. By mapping the genomic sites that OTX2 and LHX2 could bind to, they showed that 68% of those that bound LHX2 were also bound by OTX2 (864 sites in all), suggesting that they work together to promote the activity of many genes involved in RPE development and function.
A common method for finding disease-contributing genes is to perform a genome-wide association study (GWAS), which identifies genome sequence differences between individuals that share a particular disease. However, a GWAS alone cannot uncover a causal mechanism.
The researchers compared their LHX2/OTX2 binding data to GWAS data to hone in on variations affecting transcription factor binding, potentially contributing to AMD. One such binding site was located within the promoter region of a gene previously linked to AMD, called TRPM1. They found the sequence variant at that site altered the binding strength of LHX2; the "C version" bound it more strongly than the "T version," and TRPM1 gene activity was higher when the C allele was present instead of the T allele.
The researchers concluded that a regulatory module consisting of LHX2 and OTX2 controls RPE development and maintenance. The genomic analyses further link the genomic regions bound by the two developmental factors to AMD genetics. Furthermore, the previously-known increased risk of AMD from the variant identified in the GWAS is due to reduced binding of the LHX2 transcription factor to the TRPM1 gene promoter, and consequent reduction in this gene's activity.
"Our study exemplifies how delineation of tissue-specific transcriptional regulators, their binding sites across the genome, and their downstream gene-regulatory networks can provide insights into a complex disease's pathology," said Tel Aviv University co-author Ruth Ashery-Padan, PhD, in a statement.