Combining multiple maps shows novel genetic risk factors for blindness

Composite of an embryonic mouse eye cup (E14.5) labeled with antibodies against the developmental transcription factors Lhx2 (red) and Otx2 (green), and human retinal pigmented epithelium (RPE) labeled with antibodies against MITF (red) and ZO-1 (green). . (Images by Mazal Cohen-Gulkar, composites by Ruth Ashery-Padan, Ph.D.)

Combining a map of gene-regulatory loci with disease-associated loci, a new study reveals a new genetic risk factor for adult-onset macular degeneration (AMD).1

The study, published this week in Biology PLUS By lead authors Ran Elkon, Ph.D., and Ruth Asheri-Badan, Ph.D. of Tel Aviv University, Israel, and colleagues advance understanding of the leading cause of visual impairment in adults.

AMD is caused by a defect in the retinal pigmented epithelium (RPE), which is a layer of tissue sandwiched between the photoreceptors that receive light, and the choriocapillaris that nourish the retina. Given the central importance of RPE in AMD, the authors set out to explore a transcription factor (a protein that regulates certain genes) called LHX2 that, 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, suggesting that the role of LHX2 was likely that of a transcriptional activator, linked to regulatory sites on the genome to increase the activity of other genes.

The authors found that an affected gene, called OTX2, cooperated with LHX2 to regulate several genes in the RPE. By mapping the genomic sites to which OTX2 and LHX2 may bind, they showed that 68% of those that bound LHX2 were also bound to OTX2 (864 sites in total), suggesting that they likely work together to enhance the activity of a large group of genes involved. In the development of the RPE and its function.

One common way to find genes that may contribute to a disease is to perform a genome-wide association study (GWAS), which identifies genome sequence differences between individuals (termed single nucleotide polymorphisms, or SNPs) that occur with disease. Many of these studies have been previously performed in AMD. However, GWAS by itself cannot reveal a causal mechanism. Here, the authors compared LHX2/OTX2 binding data with GWAS data in order to identify differences that affected the binding of transcription factors, and thus may contribute to disease.

One of these binding sites was located within the promoter region of a gene called TRPM1, which was previously associated with AMD, and a sequence variant at this site was found to alter the binding strength of LHX2; The so-called C transcript binds it more strongly than the T transcript, and TRPM1 gene activity 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 from the variant identified in GWAS was due to reduced binding of the transcription factor LHX2 to the promoter of the TRPM1 gene, with a consequent decrease in the activity of this gene. The gene encodes a membrane ion channel, and previous studies have shown that mutations in the gene also cause visual impairment.

“Our study demonstrates how delineation of tissue-specific transcriptional regulators, their binding sites across the genome, and their gene regulatory networks can provide insights into the pathology of a complex disease,” the authors said in the news release.

Furthermore, Ashery-Padan noted in the press release that the findings reveal a regulatory unit consisting of LHX2 and OTX2 that controls the development and maintenance of the retinal pigmented epithelium, a tissue important for visual function.

It concluded that, “Genomic analyzes further link genomic regions associated with growth factors to the heritability of CMD.”


1. Cohen-Gulkar M, David A, Messika-Gold N, Eshel M, Ovadia S, Zuk-Bar N et al. (2023) The transcriptional regulatory module LHX2-OTX2 controls the differentiation of the retinal pigmented epithelium and underlies the genetic risk of age-related macular degeneration. PLoS Biol 21 (1): e3001924.

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