Evelyne Sernagor

Newcastle University | NCL · Institute of Neuroscience

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...

Individual retinal cell types exhibit semi-regular spatial patterns called retinal mosaics. Retinal ganglion cells (RGCs) and starburst amacrine cells (SACs) are known to exhibit such layouts. Mechanisms responsible for the formation of mosaics are not well understood but follow three main principles: (i) homotypic cells prevent nearby cells from a...

Microglia are the primary resident immune cells in the retina. They regulate neuronal survival and synaptic pruning making them essential for normal development. Following injury, they mediate adaptive responses and under pathological conditions they can trigger neurodegeneration exacerbating the effect of a disease. Retinal organoids derived from...

Developing neurons become spontaneously active while growing blood vessels begin to irrigate their surroundings. However, surprising little is known about early interactions between neural activity and angiogenesis. In the neonatal mouse retina, spontaneous waves of impulses sweep across the ganglion cell layer (GCL), just underneath the growing su...

Retinal drug toxicity screening is essential for the development of safe treatment strategies for a large number of diseases. To this end, retinal organoids derived from human pluripotent stem cells (hPSCs) provide a suitable screening platform due to their similarity to the human retina and the ease of generation in large-scale formats. In this st...

Retinal neurons are remarkedly diverse based on structure, function and genetic identity. Classifying these cells is a challenging task, requiring multimodal methodology. Here, we introduce a novel approach for retinal ganglion cell (RGC) classification, based on pharmacogenetics combined with immunohistochemistry and large-scale retinal electrophy...

Computing the spike-triggered average (STA) is a simple method to estimate the sensory neurons' linear receptive fields (RFs). For random, uncorrelated stimuli the STA provides an unbiased RF estimate, but in practice, white noise is not a feasible stimulus as it usually evokes only weak responses. Therefore, for a visual stimulus, it is often used...

Individual retinal cell types exhibit semi-regular spatial patterns called retinal mosaics. These mosaics enable uniform sampling of visual information and are formed to varying degrees across cell types. Retinal ganglion cells (RGC) and amacrine cells (including starburst amacrine cells (SAC)) are notably known to exhibit such layouts. Mechanisms...

Retinal neurons come in remarkable diversity based on structure, function and genetic identity. Classifying these cells is a challenging task, requiring multimodal methodology. Here, we introduce a novel approach for retinal ganglion cell (RGC) classification, based on pharmacogenetics combined with immunohistochemistry and large-scale retinal elec...

Retinal dystrophies often lead to blindness. Developing therapeutic interventions to restore vision is therefore of paramount importance. Here we demonstrate the ability of pluripotent stem cell-derived cone precursors to engraft and restore light responses in the Pde6brd1 mouse, an end-stage photoreceptor degeneration model. Our data show that up...

Retinal dystrophies often lead to blindness. Developing therapeutic interventions to restore vision is therefore of paramount importance. Here we demonstrate the ability of pluripotent stem cell-derived cone precursors to engraft and restore light responses in the Pde6brd1 mouse, an end-stage photoreceptor degeneration model. Up to 1.5% of precurso...

This manuscript has been withdrawn by the authors as they no longer stand by part of their conclusions and wish not to be cited for this work. If you have any questions, please contact the corresponding authors.

Chronic pain is a global healthcare problem with a huge societal impact. Its management remains unsatisfactory, with no single treatment clinically approved in most cases. In this study we use an in vitro experimental model of erythromelalgia consisting of sensory neurons derived from human induced pluripotent stem cells obtained from a patient (ca...

The generation of laminated and light responsive retinal organoids from induced pluripotent stem cells (iPSCs) provides a powerful tool for the study of retinal diseases and drug discovery and a robust platform for cell-based therapies. The aim of this study is to investigate whether retinal organoids can retain their morphological and functional c...

Waves of spontaneous activity sweep across the neonatal mouse retinal ganglion cell (RGC) layer, driven by directly interconnected cholinergic starburst amacrine cells (the only known retinal cholinergic cells) from postnatal day (P) 0-10, followed by waves driven by glutamatergic bipolar cells. We found transient clusters of cholinergic RGC-like c...

Induced pluripotent stem cell (iPSC)-derived retinal organoids provide a platform to study human retinogenesis, disease modelling and compound screening. Whilst retinal organoids may represent tissue structures with greater physiological relevance to the in vivo human retina, their generation is not without limitations. Various protocols have been...

Figure S2: CRX‐GFP + cells within cluster 1 and 2 show a similar expression of rod precursor marker NRL. A) Expression of NRL in cluster 1 and 2 shown through a violin plot profile; B) Immunostaining of retinal organoids at day 90 showing few GFP+ cells co‐stained with NRL (white arrows); B′) Inset: high magnification of NRL+ and CRX‐GFP+ cell. Sca...

Figure S1: Stepwise filtering strategy of single cell RNA‐Seq data. A and B) Cells which had fewer than 150,000 reads or 2,000 genes were removed from downstream analysis; C) Cells with housekeeping genes of less than 20,000 counts were removed from analysis; D) Cells with higher than 10% mitochondrial genes were removed from analysis; E) Cells wit...

Figure S3: CRX‐GFP + cells within cluster 1 show a cone biased transcriptional profile. A) Expression of ONECUT1, OLIG2 and OTX2 cone markers in cluster 1 and 2 shown through violin plot profiles; B) Immunostaining of retinal organoids at day 90 showing co‐staining of CRX‐GFP+ cells with OTX2; very few CRX‐GFP+ cells co‐localize with ONECUT1 (white...

Table S1: Summary of antibodies used for immunohistochemical staining.

Figure S4: Characterization of Pde6brd1 Mouse Model of Retinal Degeneration compared with Wild Type Mouse Retina. IHC imaged showing the different localization of retinal markers in Pde6brd1 Mouse Model of Retinal Degeneration and C57 Wild Type Mouse (WT). A‐B) Localization of pan‐photoreceptor marker (Recoverin) in WT retina in the OS/IS and ONL (...

Table S2: List of significantly and differentially expressed genes between clusters 1 and 2.

Tissue specific extracellular matrices (ECM) provide structural support and enable access to molecular signals and metabolites, which are essential for directing stem cell renewal and differentiation. To mimic this phenomenon in vitro, tissue decellularisation approaches have been developed, resulting in the generation of natural ECM scaffolds that...

A major goal in the stem cell field is to generate tissues which can be utilized as a universal tool for in vitro models of development and disease, drug development, or as a resource for patients suffering from disease or injury. Great efforts are being made to differentiate human pluripotent stem cells in vitro toward retinal tissue, which is aki...

Death of photoreceptors is a common cause of age-related and inherited retinal dystrophies, thus their replenishment from renewable stem cell sources is a highly desirable therapeutic goal. Human pluripotent stem cells provide a useful cell source in view of their limitless self-renewal capacity and potential to differentiate not only into cells of...

Retinal ganglion cells, the sole output neurons of the retina, exhibit surprising diversity. A recent study reported over 30 distinct types in the mouse retina, indicating that the processing of visual information is highly parallelised in the brain. The advent of high density multi-electrode arrays now enables recording from many hundreds to thous...

Mutations in pre-mRNA processing factors (PRPFs) cause autosomal-dominant retinitis pigmentosa (RP), but it is unclear why mutations in ubiquitously expressed genes cause non-syndromic retinal disease. Here, we generate transcriptome profiles from RP11 (PRPF31-mutated) patient-derived retinal organoids and retinal pigment epithelium (RPE), as well...

Figure S1. Brightfield images of organoids. Example images of organoids cultured in pooled and single conditions from each cell line tested. Scale bar = 500 μM.

Figure S4. TEM and electrophysiological analysis. (A): Transmission electron micrographs of single and (B) pooled retinal organoids at day 150. Abbreviations: OLM, outer limiting membrane; IS, inner segment; PC, primary cilium; M, mitochondria; OS, outer segment. Scale bar far left = 2 μm, scale bar middle and right = 500 nm. (C): 25 representative...

Figure S5. Factorial experimental design. (A): Table showing design of factorial experiment 1. (B): Table showing design of factorial experiment 2. (C): Chart showing overlapping coverage of cell number and BMP4 between the two experiments.

Figure S2. Relative organoid size during the differentiation process. Error bars = SEM. Significance assessed by one way ANOVA with Tukey's multiple comparisons test.

Figure S6. Response of iPSC‐derived‐retinal organoids to moxifloxacin treatment. (A): Hematoxylin and eosin staining of retinal organoids, left = untreated control and right = Moxifloxacin 100 μg/ml. Red asterisk = disorganization and gaps in laminated structure (Scale bar = 100 μm; n = 3). (B): LDH tests of retinal organoids treated with Moxifloxa...

Table S1. The DNA sequence of oligonucleotides used in the qRT‐PCR analysis.

Table S2. Summary of antibodies used in this study.

Figure S3. Schematic chart showing the development of iPSC derived retinal organoids and RPE spheres at day 60 of differentiation. Abbreviations: RPE, RPE spheres; NR, retinal organoids with neural retina (no RPE), NR+ RPE, retinal organoids with RPE; undefined, organoids that did not contain any neural retina or RPE cells, n = 3.

Table S5. (A): Table showing significant single interactions on gene expression for design 2. (B): Table showing two way interactions for design 2.

Table S3. Mann–Whitney U test on spiking activity.

Table S4. (A): Table showing significant single interactions on gene expression for design 1. (B): Table showing two way interactions for design 1.

Retinal ganglion cells, the sole output neurons of the retina, exhibit surprising diversity. A recent study reported over 30 distinct types in the mouse retina, indicating that the processing of visual information is highly parallelised in the brain. The advent of high density multi-electrode arrays now enables recording from many hundreds to thous...

Objective: Our main objective is to demonstrate that compact high radiance gallium nitride displays can be used with conventional virtual reality optics to stimulate an optogenetic retina. Hence, we aim to introduce a non-invasive approach to restore vision for people with conditions such as retinitis pigmentosa where there is a remaining viable c...

The availability of in vitro models of the human retina in which to perform pharmacological and toxicological studies is an urgent and unmet need. An essential step for developing in vitro models of human retina is the ability to generate laminated, physiologically functional and light-responsive retinal organoids from renewable and patient specifi...

Automatic detection and segmentation of neurons from microscopy acquisition is essential for statistically characterizing neuron morphology that can be related to their functional role. In this paper, we propose a combined pipeline that starts from the automatic detection of the soma through a new multiscale blob enhancement filtering. Then, a prec...

It is well established that the Ca2+ binding proteins parvalbumin (PV) and calretinin (CR) are widely expressed in retinal ganglion cells (RGCs) and amacrine cells (ACs). Most of the current knowledge on these cells arises from studies focused on either PV or CR expression, but virtually nothing is known about PV and CR co-expression in different r...

Mutations in pre-mRNA processing factors (PRPFs) cause 40% of autosomal dominant retinitis pigmentosa (RP), but it is unclear why mutations in ubiquitously expressed PRPFs cause retinal disease. To understand the molecular basis of this phenotype, we have generated RP type 11 (PRPF31-mutated) patient-specific retinal organoids and retinal pigment e...

We present a method for automated spike sorting for recordings with high-density, large-scale multielectrode arrays. Exploiting the dense sampling of single neurons by multiple electrodes, an efficient, low-dimensional representation of detected spikes consisting of estimated spatial spike locations and dominant spike shape features is exploited fo...

We have investigated the ontogeny of light-driven responses in mouse retinal ganglion cells (RGCs). Using a large-scale, high-density multielectrode array, we recorded from hundreds to thousands of RGCs simultaneously at pan-retinal level, including dorsal and ventral locations. Responses to different contrasts not only revealed a complex developme...

The choice of electrode material is of paramount importance in neural prosthetic devices. Electrodes must be biocompatible yet able to sustain repetitive current injections in a highly corrosive environment. We explored the suitability of carbon nanotube (CNT) electrodes to stimulate retinal ganglion cells (RGCs) in a mouse model of outer retinal d...

Retinitis pigmentosa is a progressive retinal dystrophy that causes irreversible visual impairment and blindness. Retinal prostheses currently represent the only clinically available vision-restoring treatment, but the quality of vision returned remains poor. Recently, it has been suggested that the pathological spontaneous hyperactivity present in...

How a population of retinal ganglion cells (RGCs) encodes the visual scene remains an open question. Going beyond individual RGC coding strategies, results in salamander suggest that the relative latencies of an RGC pair encodes spatial information. Thus a population code based on this concerted spiking could be a powerful mechanism to transmit vis...

The choice of electrode material is of paramount importance in neural prosthetic devices. Electrodes must be biocompatible yet able to sustain repetitive current injections in a highly corrosive environment. We explored the suitability of carbon nanotube (CNT) electrodes to stimulate retinal ganglion cells (RGCs) in a mouse model of outer retinal d...

We have investigated the ontogeny of light-driven responses in mouse retinal ganglion cells (RGCs). Using a large-scale, high-density multielectrode array, we recorded from hundreds to thousands of RGCs simultaneously at pan-retinal level, including dorsal and ventral locations. Responses to different contrasts not only revealed a complex developme...

A new method for automated spike sorting for recordings with high density, large scale multielectrode arrays is presented. It is based on an efficient, low-dimensional representation of detected events by their estimated spatial current source locations and dominant spike shape features. Millions of events can be sorted in just minutes, and the ful...

An emerging generation of high-density microelectrode arrays (MEAs) is now capable of recording spiking activity simultaneously from thousands of neurons with closely spaced electrodes. Reliable spike detection and analysis in such recordings is challenging due to the large amount of raw data and the dense sampling of spikes with closely spaced ele...

Retinitis pigmentosa (RP) is a progressive retinal dystrophy that causes visual impairment and eventual blindness. Retinal prostheses are the best currently available vision-restoring treatment for RP, but only restore crude vision. One possible contributing factor to the poor quality of vision achieved with prosthetic devices is the pathological r...

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