The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration

PLoS Biol. 2023 Jan 17;21(1):e3001924. doi: 10.1371/journal.pbio.3001924. eCollection 2023 Jan.


Tissue-specific transcription factors (TFs) control the transcriptome through an association with noncoding regulatory regions (cistromes). Identifying the combination of TFs that dictate specific cell fate, their specific cistromes and examining their involvement in complex human traits remain a major challenge. Here, we focus on the retinal pigmented epithelium (RPE), an essential lineage for retinal development and function and the primary tissue affected in age-related macular degeneration (AMD), a leading cause of blindness. By combining mechanistic findings in stem-cell-derived human RPE, in vivo functional studies in mice and global transcriptomic and proteomic analyses, we revealed that the key developmental TFs LHX2 and OTX2 function together in transcriptional module containing LDB1 and SWI/SNF (BAF) to regulate the RPE transcriptome. Importantly, the intersection between the identified LHX2-OTX2 cistrome with published expression quantitative trait loci, ATAC-seq data from human RPE, and AMD genome-wide association study (GWAS) data, followed by functional validation using a reporter assay, revealed a causal genetic variant that affects AMD risk by altering TRPM1 expression in the RPE through modulation of LHX2 transcriptional activity on its promoter. Taken together, the reported cistrome of LHX2 and OTX2, the identified downstream genes and interacting co-factors reveal the RPE transcription module and uncover a causal regulatory risk single-nucleotide polymorphism (SNP) in the multifactorial common blinding disease AMD.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation
  • DNA-Binding Proteins / metabolism
  • Epithelium / metabolism
  • Genome-Wide Association Study
  • Humans
  • LIM Domain Proteins / genetics
  • LIM Domain Proteins / metabolism
  • LIM-Homeodomain Proteins / genetics
  • LIM-Homeodomain Proteins / metabolism
  • Macular Degeneration* / genetics
  • Macular Degeneration* / metabolism
  • Mice
  • Otx Transcription Factors / genetics
  • Otx Transcription Factors / metabolism
  • Proteomics
  • TRPM Cation Channels* / genetics
  • Transcription Factors / genetics
  • Transcription Factors / metabolism


  • LIM-Homeodomain Proteins
  • LHX2 protein, human
  • Transcription Factors
  • TRPM1 protein, human
  • TRPM Cation Channels
  • OTX2 protein, human
  • Otx Transcription Factors
  • Ldb1 protein, mouse
  • DNA-Binding Proteins
  • LIM Domain Proteins
  • Lhx2 protein, mouse
  • Otx2 protein, mouse

Grants and funding

RA-P laboratory is supported by grants from the Israel Science Foundation (1128/20), Binational Science Foundation (2013016) and European Union COST program under COST Action CA-18116, ANIRIDIA-NET supported (in part) by grant no. 317652 from the Chief Scientist Office of the Ministry of Health, Israel and the Cancer Biology Research Center, Tel Aviv University. RA-P and RE are supported by the Israel Ministry of Science (3-17557). MC’s PhD scholarship is supported by the Claire and Amedee Maratier Institute for the Study of Blindness and Visual Disorders, Sackler Faculty of Medicine, Tel Aviv University, Israel. R.E. is a Faculty Fellow of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. ME was supported in part by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.