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In-depth examination of an iPSC-derived model of human eye development identifies multiple embryonic cell types of critical importance to ocular genesis and disease

ABSTRACT: Human ocular cell cultures commonly used for disease modeling recapitulate later stages of specialized tissue differentiation, requiring the development of new models to test genetic variants affecting earlier embryonic time points. Here we provide an in-depth characterization of a recently presented 2D model mimicking whole eye development derived from human iPSCs, known as SEAMs. Our study focused on evaluating both morphological and transcriptomic changes occurring at several time points as SEAMs formed over the course of a 28-day differentiation process, with an emphasis on an intermediate stage (Day 14) and a late stage (Day 28) of SEAM development. Transcriptomic profiling using bulk and single cell RNA sequencing was followed by clustering/annotation, pathway enrichment, ligand-receptor interaction, and differentiation trajectory analyses. Bulk RNA sequencing identified 7 major expression trends and their drivers across all time points. Single cell analyses revealed 12 and 14 partially overlapping, yet distinct clusters at Day 14 and 28, respectively, showing a progression from less (optic cup and anterior segment precursors) to more (mature retina, retinal pigmented epithelium, lens, and cornea, including limbal epithelial stem cells) differentiated cell types based on characteristic transcriptional signatures, corroborated by pseudotime and RNA velocity analyses. Establishment of a temporal baseline of SEAM development enables future investigations into how disease-causing variants may disrupt the early stages of human eye development leading to complex ocular phenotypes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE290847 | GEO | 2025/06/16

REPOSITORIES: GEO

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Project description:MicroRNA expression in the mouse eye.MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution. In this report, we present the first comprehensive survey of miRNA expression in ocular tissues, using both microarray and RNA in situ hybridization (ISH) procedures. We initially determined the expression profiles of miRNAs in the retina, lens, cornea and retinal pigment epithelium of the adult mouse eye by microarray. Each tissue exhibited notably distinct miRNA enrichment patterns and cluster analysis identified groups of miRNAs that showed predominant expression in specific ocular tissues or combinations of them. Next, we performed RNA ISH for over 220 miRNAs, including those showing the highest expression levels by microarray, and generated a high-resolution expression atlas of miRNAs in the developing and adult wild-type mouse eye, which is accessible in the form of a publicly available web database. We found that 122 miRNAs displayed restricted expression domains in the eye at different developmental stages, with the majority of them expressed in one or more cell layers of the neural retina . This analysis revealed miRNAs with differential expression in ocular tissues and provided a detailed atlas of their tissue-specific distribution during development of the murine eye. The combination of the two approaches offers a valuable resource to decipher the contributions of specific miRNAs and miRNA clusters to the development of distinct ocular structures. microRNA profiling of ocular tissues from mouse. In particular we analysed the cornea, lens, Retina Pigment Epithelium (RPE) and retina and compared them against RNA extracted from the entire eye. The purpose of this experiment was to understand which microRNAs are present nd/or show differential expression in the various structures of the eye (cornea, lens, RPE, retina). The samples numbered 1 & 2 (i.e. CORNEA1, CORNEA2 etc ) are biological replicates, prepared from tissues dissecyed from different groups of wild-type animals. RNA extracted from the entire eye (EYE) served as the unique reference sample. For each tissue to be analysed we performed the following hybridizations: - 2 slides for lens (LENS1, LENS2) vs entire eye (EYE) - 2 slides for RPE (RPE1, RPE2) vs entire eye (EYE) - 2 slides for retina (RETINA1, RETINA2) vs entire eye (EYE) - 2 slides for cornea (CORNEA1, CORNEA2) vs entire eye (EYE) - 1 slide for entire eye (EYE) vs entire eye (EYE)

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In-depth examination of an iPSC-derived model of human eye development identifies multiple embryonic cell types of critical importance to ocular genesis and disease

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