RNA-seq

Ocular coloboma (OC) is a failure of complete optic fissure closure during embryonic development and presents as a tissue defect along the proximal distal axis of the ventral eye. It is classed as part of the clinical spectrum of structural eye malformations with microphthalmia and anophthalmia, collectively abbreviated to MAC. Despite deliberate attempts to identify causative variants in MAC, many patients remain without a genetic diagnosis. To reveal potential candidate genes, we utilised transcriptomes experimentally generated from embryonic eye tissues derived from human, mouse, zebrafish, and chicken at stages coincident with optic fissure closure

The crumbs cell polarity complex plays a crucial role in apical-basal epithelial polarity, cellular adhesion, and morphogenesis. Homozygous variants in human CRB1 result in autosomal recessive Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP), with no established genotype-phenotype correlation. We performed integrative transcriptomic and methylomic analysis of whole retina to identify dysregulated genes and pathways.

Investigation of the molecular pathology of oculogenesis regulator, PAX6, through patient-derived hiPSC optic vesicles with (i) haploinsufficiency-related aniridia and (ii) missense-associated microphthalmia. Transcriptomic analysis reveals variant-specific disruption to SOX2-mediated Notch-signalling perturbing proliferation and differentiation, uncovering a mechanism for PAX6-associated microphthalmia.

The homeostasis of the transparent corneal epithelium in the eye is maintained by limbal stem cells with proper cell fates. A potential disease mechanism underlying corneal opacity has been proposed to be limbal stem cells acquiring characteristics of keratinocytes of the non-transparent epidermis. We performed a multi-omics analysis of human limbal stem cells derived from the cornea and keratinocytes from the epidermis, and characterized their similar yet distinct molecular signatures.

Single Cell Omics Workshop 2022

Cross species transcriptome analysis can be a powerful tool for identifying rare disease genes. By looking at the transcriptome of a variety of species, including humans, it is possible to identify genes that are differentially expressed in the diseased state. This can help to identify both disease-causing genes and genes that are involved in the disease process.

Ocular coloboma arises from genetic or environmental perturbations which inhibit optic fissure fusion in early eye development. Despite high genetic heterogeneity, 70-85% of patients remain molecularly undiagnosed. We report BMPR1B as a novel causative gene using cross-species comparative meta-analysis.

Eye morphogenesis is tightly regulated by a highly conserved genetic network that when disrupted, can result in severe ocular malformation on a spectrum known as microphthalmia, anophthalmia and coloboma (MAC). Using RNA-seq, we detected upregulation of pro-apoptotic genes in microphthalmia optic vesicles. Dysregulation of Notch signalling modulated through an ASCL1 negative feedback loop between the DLL ligand and HES effector families was also common between microphthalmia samples. This resulted in differential expression of Notch target genes such as MITF and HDAC1. Additionally, the increased production of extracellular matrix (ECM) components such as collagen and laminin, resulting in ECM abnormalities, was detected in microphthalmia optic vesicles.

ARVO Annual Meeting 2022

The combination of abundant data resources and cheap sequencing technology has resulted in a vast unexploited resource for single nucleotide polymorphism (SNP) detection.