Comparison of Glaucoma-Relevant Transcriptomic Datasets Identifies Novel Drug Targets for Retinal Ganglion Cell Neuroprotection

Abstract

Glaucoma is a leading cause of blindness and is characterized by the progressive dysfunction and irreversible death of retinal ganglion cells. We aimed to identify shared differentially expressed genes (DE genes) between different glaucoma relevant models of retinal ganglion cell injury using existing RNA-sequencing data, thereby discovering targets for neuroprotective therapies. A comparison of DE genes from publicly available transcriptomic datasets identified 12 shared DE genes. The Comparative Toxicogenomics Database (CTD) was screened for compounds targeting a significant proportion of the identified DE genes. Forty compounds were identified in the CTD that interact with >50% of these shared DE genes. We next validated this approach by testing select compounds for an effect on retinal ganglion cell survival using a mouse retinal explant model. Folic acid, genistein, SB-431542, valproic acid, and WY-14643 (pirinixic acid) were tested. Folic acid, valproic acid, and WY-14643 demonstrated significant protection against retinal ganglion cell death in this model. The increasing prevalence of open access-omics data presents a resource to discover targets for future therapeutic investigation.

Valproic Acid Reduces Neuroinflammation to Provide Retinal Ganglion Cell Neuroprotection in the Retina Axotomy Model

“…The retinal explant model has previously been demonstrated to be a useful tool for the rapid exploration of neurodegenerative and neuroprotective mechanisms in mouse, rat, pig, and human retina ( Bull et al, 2011 ; Bell et al, 2016 ; Binley et al, 2016 ; Osborne et al, 2016 ; Williams et al, 2017a ; Tribble et al, 2021c ; Enz, Tribble and Williams, 2021 ). Our data demonstrate that it is also highly amenable in investigating neuroinflammation without the loss of spatial interaction that occurs in cell culture or direct insult to glial and astrocytes that may occur from cutting brain slices for culture (as, in this model, only retinal ganglion cell axons are axotomized).…”

“…In the CNS, VPA has demonstrated both neuroprotective and anti-inflammatory effects in diverse animal models of neurodegenerative conditions including spinal cord injury, traumatic brain injury, stroke, Parkinson’s disease, and optic neuritis ( Kim et al, 2007 ; Liu et al, 2017 ; Chen S et al, 2018 ; Chen X et al, 2018 ; Chang et al, 2019 ; Kim et al, 2019 ). Using a comparative transcriptomics approach, we recently identified VPA as a potential modifier of expression of genes common to retinal ganglion cell axon degeneration ( Enz, Tribble and Williams, 2021 ) (the susceptible neuron in many optic neuropathies including glaucoma, Leber’s hereditary optic neuropathy, and autosomal dominant optic atrophy). Pathway analysis of genes revealed neuroinflammatory signaling pathways to be the most commonly shared element and, as hypothesized, VPA provided significant neuroprotection to retinal ganglion cells post-axotomy.…”

Differential Retinal Ganglion Cell Vulnerability, A Critical Clue for the Identification of Neuroprotective Genes in Glaucoma

“…There are many other DEGs that we were unable to cover in the scope of this review but may ultimately play important roles in neuroprotection. Several key review articles have previously organized and described relevant genes and molecular mechanisms of neurodegeneration in glaucoma (142)(143)(144). Most recently, Wang et al (145) have also summarized commonly upregulated or downregulated genes by comparing transcriptomic data in several glaucoma mouse models and optic nerve crush models, most of which we have also included in this review.…”

Gene Expression Data for Investigating Glaucoma Treatment Options and Pharmacology in the Anterior Segment, State-of-the-Art and Future Directions

“…Moreover, regarding the cornea, the first large-scale single-cell dataset was just published ( Collin et al, 2021 ). Finally, a recent meta-analysis of glaucoma-related gene expression yielded drug candidates protecting retinal ganglion cells, as described by Enz et al (2021) .…”