Biology subjects

Sampath, A. P.

Publications and source records attributed to Sampath, A. P..

5 recordsLinked to original sources

bioRxiv2024

Conservation of cis-regulatory codes over half a billion years of evolution

The identification of homologous cell types across species represents a crucial step in understanding cell type evolution. The retina is particularly amenable to comparative analysis because the basic morphology, connectivity, and function of its six major cell classes have remained largely invariant since the earliest stages of vertebrate evolution. Here, we show that the retinas highly conserved cellular architecture is mirrored by deep conservation of the underlying cis-regulatory codes that control gene expression. We use comparative single-cell chromatin accessibility analysis of lamprey, fish, bird, and mammalian retinas-- representing over half a billion years of evolutionary divergence--to demonstrate cross-species conservation of cis-regulatory codes in all six retinal cell classes. This conservation persists despite extensive turnover of cis-regulatory regions between distant species. Conservation manifests as the clustering of multiple distinct high-affinity transcription factor (TF) binding sites toward the center of cell-class-specific open chromatin regions with little cross-species preservation of higher-order syntax. Hierarchical clustering of machine-learning models of retinal cis-regulatory codes from diverse species recovers six clusters corresponding to the six retinal cell classes. Thus, the retinas cellular Bauplan is controlled by cis-regulatory codes which predate the divergence of extant vertebrates and persist despite nearly complete enhancer turnover.

evolutionary biology↗

bioRxiv2023

Molecular Characterization of the Sea Lamprey Retina Illuminates the Evolutionary Origin of Retinal Cell Types

The lamprey, a primitive jawless vertebrate whose ancestors diverged from all other vertebrates over 500 million years ago, offers a unique window into the primordial formation of the retina. Using single-cell RNA-sequencing, we characterized retinal cell types in lamprey and compared their molecular differentiation and regulatory networks with those in mouse and other jawed vertebrates. Our analysis revealed six cell classes and 74 distinct cell types. We discovered multiple conserved cell types shared between jawless and jawed lineages, including notably rods and cones, ON and OFF bipolar cells, and starburst amacrine cells. The conservation of these cell types indicates their emergence early in vertebrate evolution, highlighting the primal designs of retinal circuits for the rod pathway, ON-OFF discrimination, and direction selectivity. In contrast to this evidence for conservation, the pathways of diversification for amacrine cells and retinal ganglion cells appear to have distinctly diverged between the two lineages. Furthermore, we inferred master regulators in specifying retinal cell classes in both lamprey and macaque and identified common regulatory elements across species, underscoring the ancestral nature of the molecular origins governing retinal cell classes. Altogether, our characterization of the lamprey retina illuminates the evolutionary origin of visual processing in the retina.

evolutionary biology↗

bioRxiv2023

Late gene therapy limits the restoration of retinal function in a mouse model of retinitis pigmentosa

Retinitis pigmentosa is an inherited photoreceptor degeneration that begins with rod loss followed by cone loss and eventual blindness. Gene therapies are being developed, but it is unknown how retinal function depends on the time of intervention. To uncover this dependence, we utilized a mouse model of retinitis pigmentosa capable of artificial genetic rescue. This model enables a benchmark of best-case gene therapy by removing the variables that complicate the ability to answer this vital question. Complete genetic rescue was performed at 25%, 50%, and 70% rod loss (early, mid and late, respectively). Early and mid treatment restored retinal function to near wild-type levels, specifically the sensitivity and signal fidelity of retinal ganglion cells (RGCs), the output neurons of the retina. However, some anatomical defects persisted. Late treatment retinas exhibited continued, albeit slowed, loss of sensitivity and signal fidelity among RGCs, as well as persistent gliosis. We conclude that gene replacement therapies delivered after 50% rod loss are unlikely to restore visual function to normal. This is critical information for administering gene therapies to rescue vision.

neuroscience↗

bioRxiv2022

Cones and Cone Pathways Remain Functional in Advanced Retinal Degeneration

Most defects causing retinal degeneration in retinitis pigmentosa (RP) are rod-specific mutations, but the subsequent degeneration of cones, which produces loss of daylight vision and high-acuity perception, is the most debilitating feature of the disease. To understand better why cones degenerate and how cone vision might be restored, we have made the first single-cell recordings of light responses from degenerating cones and retinal interneurons after most rods have died and cones have lost their outer-segment disk membranes and synaptic pedicles. We show that degenerating cones have functional cyclic-nucleotide-gated channels and can continue to give light responses, apparently produced by opsin localized either to small areas of organized membrane near the ciliary axoneme or distributed throughout the inner segment. Light responses of second-order horizontal and bipolar cells are smaller and less sensitive but surprisingly similar to those of normal retina. Furthermore, retinal output as reflected in responses of ganglion cells is largely intact at cone-mediated light levels. Together, these findings show that cones and their retinal pathways can remain functional even as degeneration is progressing, an encouraging result for future research aimed at enhancing the light sensitivity of residual cones to restore vision in patients with genetically inherited retinal degeneration.

neuroscience↗

bioRxiv2018

Activation of rod input in a in a model of retinal degeneration reverses retinal remodeling and induces formation of normal synapses, circuitry and visual signaling in the adult retina

A major cause of human blindness is the death of rod photoreceptors. As rods degenerate, synaptic structures between rod and rod bipolar cells dissolve and the rod bipolar cells extend their dendrites and occasionally make aberrant contacts. Such changes are broadly observed in blinding disorders caused by photoreceptor cell death and is thought to occur in response to deafferentation. How the remodeled retinal circuit affect visual processing following rod rescue is not known. To address this question, we generated transgenic mice wherein a disrupted cGMP-gated channel (CNG) gene can be repaired at the endogenous locus and at different stages of degeneration by tamoxifen-inducible cre-mediated recombination. In normal rods, light-induced closure of CNG channels leads to hyperpolarization of the cell, reducing neurotransmitter release at the synapse. Similarly, rods lacking CNG channel exhibit a resting membrane potential that was ~10mV hyperpolarized compared to WT rods, indicating diminished glutamate release. Retinas from these mice undergo stereotypic retinal remodeling as a consequence of rod malfunction and degeneration. Upon tamoxifen-induced expression of CNG channels, rods recovered their structure and exhibited normal light responses. Moreover, we show that the adult mouse retina displays a surprising degree of plasticity upon activation of rod input. Wayward bipolar cell dendrites establish contact with rods to support normal synaptic transmission, which is propagated to the retinal ganglion cells. These findings demonstrate remarkable plasticity extending beyond the developmental period and support efforts to repair or replace defective rods in patients blinded by rod degeneration.\n\nSignificance StatementCurrent strategies for treatment of neurodegenerative disorders are focused on the repair of the primary affected cell type. However, the defective neuron functions within a complex neural circuitry, which also becomes degraded during disease. It is not known whether a rescued neuron and the remodeled circuit will establish communication to regain normal function. We show that the adult mammalian neural retina exhibits a surprising degree of plasticity following rescue of rod photoreceptors. The wayward rod bipolar cell dendrites re-establish contact with rods to support normal synaptic transmission, which is propagated to the retinal ganglion cells. These findings support efforts to repair or replace defective rods in patients blinded by rod cell loss.

neuroscience↗