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A gene expression study of the developing human eye

ABSTRACT: There is a vast range of tools with which to study the cells and tissues of the human body, however the scarcity of human embryonic material as a resource for direct study means that there is still limited data on the specific expression patterns which exist during human development. While embryonic studies are common place in other mammalian organisms and these have contributed greatly to our knowledge, characterising the events which occur during human development specifically is crucial in order to extrapolate the differences which exist between humans and other organisms and understand the human situation more completely. Establishing and maintaining collections of human developmental tissue for direct study requires significant time and resources, and is not a viable option for all. For this reason the creation of an atlas defining the key events which occur during human eye development would be of great value to the field. Through the Human Developmental Biology Resource we have collected human developmental eye tissue from post conception week 4 to 19 and performed gene expression studies using RNA sequencing. This study begins to reveal the spatiotemporal gene expression patterns which occur during normal human eye ontogenesis and represents a benchmark for comparison with development, disease and cellular differentiation studies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE98370 | GEO | 2019/01/15

REPOSITORIES: GEO

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Project description:Gene expression profiling has provided critical insights into the molecular pathways underlying development of model organisms, however little information is available on regulated gene expression during human embryogenesis. We have now filled this important gap of knowledge by performing genome-wide microarray analysis of the Homo sapiens gene expression during the 4-9th week, a period when most organs develop. We analyzed individually 3 embryos for each of the 4th, 5th, 6th, 7th, 8th, and 9th week of human embryonic development by using the Affymetrix U133 plus 2.0 human GeneChip array.About half of all human genes are expressed and 18.6% of the expressed genes were significantly regulated during this important period. We further identified over 5000 regulated genes, most of which were previously not known to be associated with animal development. Our study also revealed that the genes involved here are distinct from those during early embryogenesis, which include three groups of maternal genes. Furthermore, we discovered that genes in a given developmental process are coordinately regulated. This led us to develop an easily searchable database of this entire collection of gene expression profiles, allowing for identification new genes important for a particular developmental process/pathway and deducing the potential function of a novel gene. The validity of the predictions from the database was demonstrated with two examples through spatiotemporal analyses of the two novel genes. Such a database should serve as a highly valuable resource for the molecular analysis of human development and pathogenesis. Human embryos were obtained from therapeutic termination of pregnancy induced by Mifepristone. Morphologically normal embryos were selected and staged according to the Carnegie classification and the Chinese embryonic developmental characteristics. Each whole embryo was micro-dissected from an intact trophoblast and stored directly in liquid nitrogen or homogenized using Trizol solution and then stored at -80oC. Total RNA was isolated from each whole embryo individually and each of the 3 RNA samples for each developmental time point was independently analyzed on a Human U133 plus 2.0 Genome Oligonucleotide Array.

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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A gene expression study of the developing human eye

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