Combining a map of gene regulatory sites with disease-associated loci has uncovered a new genetic risk factor of adult macular degeneration (AMD), according to a new study published Jan. 17 in the open-access journal PLOS Biology by Ran Elkon and Ruth Ashery- Padan of Tel Aviv University, Israel, and colleagues. The finding advances understanding of the main cause of visual impairment in adults.
AMD is caused by 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. Because of the central importance of the RPE in AMD, the authors began investigating a transcription factor (a protein that regulates specific genes) called LHX2, which, based on the team’s analysis of mouse mutants, is central to the development of RPE. By knocking down LHX2 activity in RPE derived from human stem cells, they found that most of the affected genes were down-regulated, indicating that LHX2’s role was likely that of a transcriptional activator, binding to regulatory sites on the genome to increase the activity of other genes.
The authors found that one affected gene, called OTX2, interacted with LHX2 to regulate many genes in the RPE. By mapping the genomic sites to which OTX2 and LHX2 could bind, they showed that 68% of those that bound LHX2 were also bound by OTX2 (864 sites in total), suggesting that they likely work together to increase the activity of a large set of genes. involved in the development and function of RPE.
A common method of finding genes that may contribute to a disease is to perform a genome-wide association study (GWAS), which identifies genomic sequence differences between individuals (called single nucleotide polymorphisms, or SNPs) that co-occur with the disease. Numerous such studies have been done before at AMD. However, a GWAS by itself cannot reveal a causal mechanism. Here, the authors compared their LHX2/OTX2 binding data with GWAS data to map variations that affected transcription factor binding and thus may contribute to disease.
One such binding site was located in the promoter region of a gene called TRPM1, previously linked to AMD, and found that the sequence variant at that site altered the binding strength of LHX2; the so-called C version bound it more strongly than the T version, and the activity of the TRPM1 gene was higher when the C allele was present instead of the T allele.
The results of the study indicate that the previously known increased risk of AMD of the variant identified in the GWAS was due to a reduction in the binding of the LHX2 transcription factor to the TRPM1 gene promoter, resulting in a reduction in activity of this gene. . The gene codes for a membrane ion channel, and previous studies have shown that mutations in the gene also cause visual impairment.
“Our study illustrates how delineation of tissue-specific transcriptional regulators, their binding sites across the genome, and their downstream gene regulatory networks can provide insight into the pathology of a complex disease,” said the authors.
Adds Ashery-Padan: “The findings reveal a regulatory module comprised of LHX2 and OTX2 that controls the development and maintenance of the retinal pigmented epithelium, an important tissue of visual function. The genomic analyzes further link the genomic regions bound by the two developmental factors to the genetics of the common, multifactorial blinding disease age-related macular degeneration (AMD).
- Cohen-Gulkar M, David A, Messika-Gold N, Eshel M, Ovadia S, Zuk-Bar N, et al. (2023) The LHX2-OTX2 transcriptional regulatory module controls the differentiation of retinal pigmented epithelium and underlies the genetic risk for age-related macular degeneration. PLoS Biol 21(1): e3001924. DOI:10.1371/journal.pbio.3001924