RNA Biology in Retinal Development and Disease

Cell-cell interaction in the pathogenesis of inherited retinal diseases

The retina is part of the central nervous system specialized for vision. Inherited retinal diseases (IRD) are a group of clinically and genetically heterogenous disorders that lead to progressive vision impairment or blindness. Although each disorder is rare, IRD accumulatively cause blindness in up to 5.5 million individuals worldwide. Currently, the pathophysiological mechanisms of IRD are not fully understood and there are limited treatment options available. Most IRD are caused by degeneration of light-sensitive photoreceptors. Genetic mutations that abrogate the structure and/or function of photoreceptors lead to visual impairment followed by blindness caused by loss of photoreceptors. In healthy retina, photoreceptors structurally and functionally interact with retinal pigment epithelium (RPE) and Müller glia (MG) to maintain retinal homeostasis. Multiple IRD with photoreceptor degeneration as a major phenotype are caused by mutations of RPE- and/or MG-associated genes. Recent studies also reveal compromised MG and RPE caused by mutations in ubiquitously expressed ciliary genes. Therefore, photoreceptor degeneration could be a direct consequence of gene mutations and/or could be secondary to the dysfunction of their interaction partners in the retina. This review summarizes the mechanisms of photoreceptor-RPE/MG interaction in supporting retinal functions and discusses how the disruption of these processes could lead to photoreceptor degeneration, with an aim to provide a unique perspective of IRD pathogenesis and treatment paradigm. We will first describe the biology of retina and IRD and then discuss the interaction between photoreceptors and MG/RPE as well as their implications in disease pathogenesis. Finally, we will summarize the recent advances in IRD therapeutics targeting MG and/or RPE.

Pathogenic Variants in USH1G/SANS Alter Protein Interaction with Pre-RNA Processing Factors PRPF6 and PRPF31 of the Spliceosome

Pre-mRNA splicing is an essential process orchestrated by the spliceosome, a dynamic complex assembled stepwise on pre-mRNA. We have previously identified that USH1G protein SANS regulates pre-mRNA splicing by mediating the intranuclear transfer of the spliceosomal U4/U6.U5 tri-snRNP complex. During this process, SANS interacts with the U4/U6 and U5 snRNP-specific proteins PRPF31 and PRPF6 and regulates splicing, which is disturbed by variants of USH1G/SANS causative for human Usher syndrome (USH), the most common form of hereditary deaf-blindness. Here, we aim to gain further insights into the molecular interaction of the splicing molecules PRPF31 and PRPF6 to the CENTn domain of SANS using fluorescence resonance energy transfer assays in cells and in silico deep learning-based protein structure predictions. This demonstrates that SANS directly binds via two distinct conserved regions of its CENTn to the two PRPFs. In addition, we provide evidence that these interactions occur sequentially and a conformational change of an intrinsically disordered region to a short α-helix of SANS CENTn2 is triggered by the binding of PRPF6. Furthermore, we find that pathogenic variants of USH1G/SANS perturb the binding of SANS to both PRPFs, implying a significance for the USH1G pathophysiology.

Light-responsive microRNA molecules in human retinal organoids are differentially regulated by distinct wavelengths of light

Cells in the human retina must rapidly adapt to constantly changing visual stimuli. This fast adaptation to varying levels and wavelengths of light helps to regulate circadian rhythms and allows for adaptation to high levels of illumination, thereby enabling the rest of the visual system to remain responsive. It has been shown that retinal microRNA (miRNA) molecules play a key role in regulating these processes. However, despite extensive research using various model organisms, light-regulated miRNAs in human retinal cells remain unknown. Here, we aim to characterize these miRNAs. We generated light-responsive human retinal organoids that express miRNA families and clusters typically found in the retina. Using an in-house developed photostimulation device, we identified a subset of light-regulated miRNAs. Importantly, we found that these miRNAs are differentially regulated by distinct wavelengths of light and have a rapid turnover, highlighting the dynamic and adaptive nature of the human retina.

Transcriptome Analysis of Retinal and Choroidal Pathologies in Aged BALB/c Mice Following Systemic Neonatal Murine Cytomegalovirus Infection

Our previous studies have shown that systemic neonatal murine cytomegalovirus (MCMV) infection of BALB/c mice spread to the eye with subsequent establishment of latency in choroid/RPE. In this study, RNA sequencing (RNA-Seq) analysis was used to determine the molecular genetic changes and pathways affected by ocular MCMV latency. MCMV (50 pfu per mouse) or medium as control were injected intra-peritoneally (i.p.) into BALB/c mice at <3 days after birth. At 18 months post injection, the mice were euthanized, and the eyes were collected and prepared for RNA-Seq. Compared to three uninfected control eyes, we identified 321 differentially expressed genes (DEGs) in six infected eyes. Using the QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA), we identified 17 affected canonical pathways, 10 of which function in neuroretinal signaling, with the majority of DEGs being downregulated, while 7 pathways function in upregulated immune/inflammatory responses. Retinal and epithelial cell death pathways involving both apoptosis and necroptosis were also activated. MCMV ocular latency is associated with upregulation of immune and inflammatory responses and downregulation of multiple neuroretinal signaling pathways. Cell death signaling pathways are also activated and contribute to the degeneration of photoreceptors, RPE, and choroidal capillaries.

Expression and subcellular localization of USH1C/harmonin in human retina provides insights into pathomechanisms and therapy

Usher syndrome (USH) is the most common form of hereditary deaf-blindness in humans. USH is a complex genetic disorder, assigned to three clinical subtypes differing in onset, course and severity, with USH1 being the most severe. Rodent USH1 models do not reflect the ocular phenotype observed in human patients to date; hence, little is known about the pathophysiology of USH1 in the human eye. One of the USH1 genes, USH1C, exhibits extensive alternative splicing and encodes numerous harmonin protein isoforms that function as scaffolds for organizing the USH interactome. RNA-seq analysis of human retinae uncovered harmonin_a1 as the most abundant transcript of USH1C. Bulk RNA-seq analysis and immunoblotting showed abundant expression of harmonin in Müller glia cells (MGCs) and retinal neurons. Furthermore, harmonin was localized in the terminal endfeet and apical microvilli of MGCs, presynaptic region (pedicle) of cones and outer segments (OS) of rods as well as at adhesive junctions between MGCs and photoreceptor cells (PRCs) in the outer limiting membrane (OLM). Our data provide evidence for the interaction of harmonin with OLM molecules in PRCs and MGCs and rhodopsin in PRCs. Subcellular expression and colocalization of harmonin correlate with the clinical phenotype observed in USH1C patients. We also demonstrate that primary cilia defects in USH1C patient-derived fibroblasts could be reverted by the delivery of harmonin_a1 transcript isoform. Our studies thus provide novel insights into PRC cell biology, USH1C pathophysiology and development of gene therapy treatment(s).

Silencing of circular RNA‑ZYG11B exerts a neuroprotective effect against retinal neurodegeneration

Ischemic retinal diseases are the major cause of vision impairment worldwide. Currently, there are no available treatments for ischemia‑induced retinal neurodegeneration. Circular RNAs (circRNAs) have emerged as important regulators of several biological processes and human diseases. The present study investigated the role of circRNA‑ZYG11B (circZYG11B; hsa_circ_0003739) in retinal neurodegeneration. Reverse transcription quantitative polymerase chain reaction (RT‑qPCR) demonstrated that circZYG11B expression was markedly increased during retinal neurodegeneration in vivo and in vitro. Cell Counting Kit‑8, TUNEL and caspase‑3 activity assays revealed that silencing of circZYG11B was able to protect against oxidative stress‑ or hypoxic stress‑induced retinal ganglion cell (RGC) injury. Furthermore, immunofluorescence staining and hematoxylin and eosin staining revealed that silencing of circZYG11B alleviated ischemia/reperfusion‑induced retinal neurodegeneration, as indicated by reduced RGC injury and decreased retinal reactive gliosis. In addition, luciferase reporter, biotin‑coupled miRNA capture and RNA immunoprecipitation assays revealed that circZYG11B could regulate RGC function through circZYG11B/microRNA‑620/PTEN signaling. Clinically, RT‑qPCR assays demonstrated that circZYG11B expression was markedly increased in the aqueous humor of patients with glaucoma. In conclusion, circZYG11B may be considered a promising target for the diagnosis and treatment of retinal ischemic diseases.

Whole transcriptome sequencing identifies key circRNAs, lncRNAs, and miRNAs regulating neurogenesis in developing mouse retina

Background

The molecular complexity of neural retina development remains poorly studied. Knowledge of retinal neurogenesis regulation sheds light on retinal degeneration therapy exploration. Therefore, we integrated the time-series circRNA, lncRNA, miRNA, and mRNA expression profiles of the developing retina through whole-transcriptome sequencing. The key functional ncRNAs and the ceRNA network regulating retinal neurogenesis were identified.

Results

Transcriptomic analysis identified circRNA as the most variable ncRNA subtype. We screened a series of neurogenesis-related circRNAs, lncRNAs, and miRNAs using different strategies based on their diversified molecular functions. The expression of circCDYL, circATXN1, circDYM, circPRGRIP, lncRNA Meg3, and lncRNA Vax2os was validated by quantitative real-time PCR. These circRNAs and lncRNAs participate in neurotransmitter transport and multicellular organism growth through the intricate circRNA/lncRNA-miRNA-mRNA network.

Conclusion

Whole-transcriptome sequencing and bioinformatics analysis systematically screened key ncRNAs in retinal neurogenesis. The validated ncRNAs and their circRNA/lncRNA-miRNA-mRNA network involve neurotransmitter transport and multicellular organism growth during retinal development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08078-z.

Functional Evaluation of Splicing for Variants of Uncertain Significance in Patients with Inherited Retinal Diseases

Inherited retinal diseases (IRD) comprise a heterogeneous set of clinical and genetic disorders that lead to blindness. Given the emerging opportunities in precision medicine and gene therapy, it has become increasingly important to determine whether DNA variants with uncertain significance (VUS) are responsible for patients’ IRD. This research was performed to assess the functional consequence of six VUS identified in patients with IRD. Clinical assessments included an ophthalmic examination, best-corrected visual acuity, and kinetic perimetry. Imaging was acquired with the Optos ultra-widefield camera and spectral domain optical coherence tomography (SD-OCT). Genetic testing was performed by Molecular Vision Laboratories. VUS that were predicted to alter splicing were analyzed with a minigene assay, which revealed that VUS in the genes OPA1, CNGB1, and CLUAP1 altered spicing mechanisms. Due to emerging gene and cell therapies, these results expand the genotype-phenotype correlations for patients diagnosed with an IRD.

Setd1a Plays Pivotal Roles for the Survival and Proliferation of Retinal Progenitors via Histone Modifications of Uhrf1

Purpose

The trimethylation of histone H3 at lysine 4 (H3K4me3) facilitates transcriptional gene activation, and Setd1a is the methyltransferase specific to H3K4. H3K4me3 has been reported to regulate rod photoreceptor differentiation; however, the roles H3K4me3 plays in retinal progenitor cell (RPC) proliferation and differentiation during early retinal development remain unclear.

Methods

Using an in vitro retinal explant culture system, we suppressed the expression of Setd1a by introducing shSetd1a. We examined the expression level and H3K4me3 level of genes by RNA Sequencing and ChIP assay, respectively.

Results

We found that Setd1a depletion resulted in increased apoptosis and proliferation failure in late RPCs. Expression of wild-type SETD1A, but not SETD1A that lacked the catalytic SET domain, reversed the shSetd1a-induced phenotype. RNA Sequencing revealed that proliferation-related genes were downregulated upon shSetd1a expression. Based on publicly available H3K4me3-ChIP sequencing data of retinal development, we identified Uhrf1 as a candidate target gene of Setd1a. The expression of shSetd1a led to a decrease in Uhrf1 transcript levels and reduced H3K4me3 levels at the Uhrf1 locus. Increased apoptosis and the suppression of proliferation in late RPCs were observed in retinal explants expressing shUhrf1, similar to the outcomes observed in shSetd1a-expressing retinas. The overexpression of UHRF1 did not rescue shSetd1a-induced apoptosis, but reversed the suppression of proliferation.

Conclusions

These results indicate that Setd1a contributes to the survival and proliferation of retinal cells by regulating histone methylation, Setd1a regulates Uhrf1 expression, and these two molecules cooperate to regulate RPC survival and proliferation.

Crystallin gene expression: Insights from studies of transcriptional bursting

Cellular differentiation is marked by temporally and spatially regulated gene expression. The ocular lens is one of the most powerful mammalian model system since it is composed from only two cell subtypes, called lens epithelial and fiber cells. Lens epithelial cells differentiate into fiber cells through a series of spatially and temporally orchestrated processes, including massive production of crystallins, cellular elongation and the coordinated degradation of nuclei and other organelles. Studies of transcriptional and posttranscriptional gene regulatory mechanisms in lens provide a wide range of opportunities to understand global molecular mechanisms of gene expression as steady-state levels of crystallin mRNAs reach very high levels comparable to globin genes in erythrocytes. Importantly, dysregulation of crystallin gene expression results in lens structural abnormalities and cataracts. The mRNA life cycle is comprised of multiple stages, including transcription, splicing, nuclear export into cytoplasm, stabilization, localization, translation and ultimate decay. In recent years, development of modern mRNA detection methods with single molecule and single cell resolution enabled transformative studies to visualize the mRNA life cycle to generate novel insights into the sequential regulatory mechanisms of gene expression during embryogenesis. This review is focused on recent major advancements in studies of transcriptional bursting in differentiating lens fiber cells, analysis of nascent mRNA expression from bi-directional promoters, transient nuclear accumulation of specific mRNAs, condensation of chromatin prior lens fiber cell denucleation, and outlines future studies to probe the interactions of individual mRNAs with specific RNA-binding proteins (RBPs) in the cytoplasm and regulation of translation and mRNA decay.

Jmjd3 Plays Pivotal Roles in the Proper Development of Early-Born Retinal Lineages: Amacrine, Horizontal, and Retinal Ganglion Cells

Purpose

Trimethylation of histone H3 at lysine 27 (H3K27me3) is a critical mediator of transcriptional gene repression, and Jmjd3 and Utx are the demethylases specific to H3K27me3. Using an in vitro retinal explant culture system, we previously revealed the role of Jmjd3 in the development of rod bipolar cells; however, the roles of Jmjd3 in the development of early-born retinal cells are unknown due to limitations concerning the use of retinal explant culture systems. In this study, we investigated the roles of Jmjd3 in the development of early-born retinal cells.

Methods

We examined retina-specific conditional Jmjd3 knockout (Jmjd3-cKO) mice using immunohistochemistry and quantitative reverse transcription PCR and JMJD3 binding to a target locus by chromatin immunoprecipitation analysis.

Results

We observed reductions in amacrine cells (ACs) and horizontal cells (HCs), as well as lowered expression levels of several transcription factors involved in the development of ACs and HCs in the Jmjd3-cKO mouse retina. JMJD3 bound the promoter regions of these transcription factors. Notably, an elevated number of retinal ganglion cells (RGCs) was observed at embryonic stages, whereas RGCs were moderately reduced at later postnatal stages in the Jmjd3-cKO retina. We also observed reduced expression of Eomes, which is required for the maintenance of RGCs, as well as lower H3K27me3 level and lower JMJD3 binding in the promoter region of Eomes in RGC-enriched cells.

Conclusions

The results indicated that Jmjd3 has critical roles in the development of early-born retinal subtypes, and suggested biphasic roles of Jmjd3 in RGC production and maintenance.

RNA sequencing analysis of the human retina and associated ocular tissues

The retina is a stratified layer of sensory neurons lining the posterior portion of the eye. In humans, fine detail and color vision are enabled by the macula, a central region of the retina dense in cone photoreceptors (PRs). Achromatic low light and peripheral vision are facilitated by rod PRs found with increasing density outside the macula in the peripheral retina. The outer retina is nourished by choroidal blood flow regulated by a single layer of intervening retinal pigment epithelial (RPE) cells. Existing human retinal transcriptome projects have been critical for studying aspects of retinal development and disease however, there are currently no publicly available data sets accurately describing the aging human central retina, peripheral retina, and supporting RPE/choroid. Here we used Illumina RNA sequencing (RNA-seq) analysis to characterize the mRNA transcriptome of rod and cone PR-enriched human retina as well as supporting macular RPE/choroid tissue. These data will be valuable to the vision research community for characterizing global changes in gene expression in clinically relevant ocular tissues.

Splicing mutations in inherited retinal diseases

Mutations which induce aberrant transcript splicing represent a distinct class of disease-causing genetic variants in retinal disease genes. Such mutations may either weaken or erase regular splice sites or create novel splice sites which alter exon recognition. While mutations affecting the canonical GU-AG dinucleotides at the splice donor and splice acceptor site are highly predictive to cause a splicing defect, other variants in the vicinity of the canonical splice sites or those affecting additional cis-acting regulatory sequences within exons or introns are much more difficult to assess or even to recognize and require additional experimental validation. Splicing mutations are unique in that the actual outcome for the transcript (e.g. exon skipping, pseudoexon inclusion, intron retention) and the encoded protein can be quite different depending on the individual mutation. In this article, we present an overview on the current knowledge about and impact of splicing mutations in inherited retinal diseases. We introduce the most common sub-classes of splicing mutations including examples from our own work and others and discuss current strategies for the identification and validation of splicing mutations, as well as therapeutic approaches, open questions, and future perspectives in this field of research.

Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss

Inherited retinal degeneration (RD) leads to the impairment or loss of vision in millions of individuals worldwide, most frequently due to the loss of photoreceptor (PR) cells. Animal models, particularly the laboratory mouse, have been used to understand the pathogenic mechanisms that underlie PR cell loss and to explore therapies that may prevent, delay, or reverse RD. Here, we reviewed entries in the Mouse Genome Informatics and PubMed databases to compile a comprehensive list of monogenic mouse models in which PR cell loss is demonstrated. The progression of PR cell loss with postnatal age was documented in mutant alleles of genes grouped by biological function. As anticipated, a wide range in the onset and rate of cell loss was observed among the reported models. The analysis underscored relationships between RD genes and ciliary function, transcription-coupled DNA damage repair, and cellular chloride homeostasis. Comparing the mouse gene list to human RD genes identified in the RetNet database revealed that mouse models are available for 40% of the known human diseases, suggesting opportunities for future research. This work may provide insight into the molecular players and pathways through which PR degenerative disease occurs and may be useful for planning translational studies.

Inherited Eye Diseases with Retinal Manifestations through the Eyes of Homeobox Genes

Retinal development is under the coordinated control of overlapping networks of signaling pathways and transcription factors. The paper was conceived as a review of the data and ideas that have been formed to date on homeobox genes mutations that lead to the disruption of eye organogenesis and result in inherited eye/retinal diseases. Many of these diseases are part of the same clinical spectrum and have high genetic heterogeneity with already identified associated genes. We summarize the known key regulators of eye development, with a focus on the homeobox genes associated with monogenic eye diseases showing retinal manifestations. Recent advances in the field of genetics and high-throughput next-generation sequencing technologies, including single-cell transcriptome analysis have allowed for deepening of knowledge of the genetic basis of inherited retinal diseases (IRDs), as well as improve their diagnostics. We highlight some promising avenues of research involving molecular-genetic and cell-technology approaches that can be effective for IRDs therapy. The most promising neuroprotective strategies are aimed at mobilizing the endogenous cellular reserve of the retina.

Retina Development in Vertebrates: Systems Biology Approaches to Understanding Genetic Programs: On the Contribution of Next-Generation Sequencing Methods to the Characterization of the Regulatory Networks Controlling Vertebrate Eye Development

The ontogeny of the vertebrate retina has been a topic of interest to developmental biologists and human geneticists for many decades. Understanding the unfolding of the genetic program that transforms a field of progenitors cells into a functionally complex and multi-layered sensory organ is a formidable challenge. Although classical genetic studies succeeded in identifying the key regulators of retina specification, understanding the architecture of their gene network and predicting their behavior are still a distant hope. The emergence of next-generation sequencing platforms revolutionized the field unlocking the access to genome-wide datasets. Emerging techniques such as RNA-seq, ChIP-seq, ATAC-seq, or single cell RNA-seq are used to characterize eye developmental programs. These studies provide valuable information on the transcriptional and cis-regulatory profiles of precursors and differentiated cells, outlining the trajectories that connect each intermediate state. Here, recent systems biology efforts are reviewed to understand the genetic programs shaping the vertebrate retina.

Generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids

Rod and cone photoreceptors are light-sensing cells in the human retina. Rods are dominant in the peripheral retina, whereas cones are enriched in the macula, which is responsible for central vision and visual acuity. Macular degenerations affect vision the most and are currently incurable. Here we report the generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids differentiated from hESCs using an improved retinal differentiation system. Induced by extracellular matrix, aggregates of hESCs formed single-lumen cysts composed of epithelial cells with anterior neuroectodermal/ectodermal fates, including retinal cell fate. Then, the cysts were en bloc-passaged, attached to culture surface, and grew, forming colonies in which retinal progenitor cell patches were found. Following gentle cell detachment, retinal progenitor cells self-assembled into retinal epithelium-retinal organoid-that differentiated into stratified cone-rich retinal tissue in agitated cultures. Electron microscopy revealed differentiating outer segments of photoreceptor cells. Bulk RNA-sequencing profiling of time-course retinal organoids demonstrated that retinal differentiation in vitro recapitulated in vivo retinogenesis in temporal expression of cell differentiation markers and retinal disease genes, as well as in mRNA alternative splicing. Single-cell RNA-sequencing profiling of 8-mo retinal organoids identified cone and rod cell clusters and confirmed the cone enrichment initially revealed by quantitative microscopy. Notably, cones from retinal organoids and human macula had similar single-cell transcriptomes, and so did rods. Cones in retinal organoids exhibited electrophysiological functions. Collectively, we have established cone-rich retinal organoids and a reference of transcriptomes that are valuable resources for retinal studies.

Identification of novel transcripts and peptides in developing murine lens

We previously investigated the transcriptome and proteome profiles of the murine ocular lens at six developmental time points including two embryonic (E15 and E18) and four postnatal time points (P0, P3, P6, and P9). Here, we extend our analyses to identify novel transcripts and peptides in developing  mouse lens. We identified a total of 9,707 novel transcripts and 325 novel fusion genes in developing mouse lens. Additionally, we identified 13,281 novel alternative splicing (AS) events in mouse lens including 6,990 exon skipping (ES), 2,447 alternative 3' splice site (A3SS), 1,900 alternative 5' splice site (A5SS), 1,771 mutually exclusive exons (MXE), and 173 intron retention (IR). Finally, we integrated our OMIC (Transcriptome and Proteome) datasets identifying 20 novel peptides in mouse lens. All 20 peptides were validated through matching MS/MS spectra of synthetic peptides. To the best of our knowledge, this is the first report integrating OMIC datasets to identify novel peptides in developing murine lens.

Epigenetic control of gene regulation during development and disease: A view from the retina

Complex biological processes, such as organogenesis and homeostasis, are stringently regulated by genetic programs that are fine-tuned by epigenetic factors to establish cell fates and/or to respond to the microenvironment. Gene regulatory networks that guide cell differentiation and function are modulated and stabilized by modifications to DNA, RNA and proteins. In this review, we focus on two key epigenetic changes - DNA methylation and histone modifications - and discuss their contribution to retinal development, aging and disease, especially in the context of age-related macular degeneration (AMD) and diabetic retinopathy. We highlight less-studied roles of DNA methylation and provide the RNA expression profiles of epigenetic enzymes in human and mouse retina in comparison to other tissues. We also review computational tools and emergent technologies to profile, analyze and integrate epigenetic information. We suggest implementation of editing tools and single-cell technologies to trace and perturb the epigenome for delineating its role in transcriptional regulation. Finally, we present our thoughts on exciting avenues for exploring epigenome in retinal metabolism, disease modeling, and regeneration.