scholarly journals A computational pipeline for functional gene discovery

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aolani Colon ◽  
Rishabh Hirday ◽  
Ami Patel ◽  
Amrita Poddar ◽  
Emma Tuberty-Vaughan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Outer Segment ◽  
Gene Discovery ◽  
Immunohistochemical Analysis ◽  
Transcriptome Profiling ◽  
Photoreceptor Cells ◽  
Functional Gene ◽  
Mouse Retina ◽  
Computational Pipeline ◽  
Photoreceptor Outer Segment

AbstractMany computational pipelines exist for the detection of differentially expressed genes. However, computational pipelines for functional gene detection rarely exist. We developed a new computational pipeline for functional gene identification from transcriptome profiling data. Key features of the pipeline include batch effect correction, clustering optimization by gap statistics, gene ontology analysis of clustered genes, and literature analysis for functional gene discovery. By leveraging this pipeline on RNA-seq datasets from two mouse retinal development studies, we identified 7 candidate genes involved in the formation of the photoreceptor outer segment. The expression of top three candidate genes (Pde8b, Laptm4b, and Nr1h4) in the outer segment of the developing mouse retina were experimentally validated by immunohistochemical analysis. This computational pipeline can accurately predict novel functional gene for a specific biological process, e.g., development of the outer segment and synapses of the photoreceptor cells in the mouse retina. This pipeline can also be useful to discover functional genes for other biological processes and in other organs and tissues.

scholarly journals A Computational Pipeline for Functional Gene Discovery

2021 ◽  
Author(s):  
Aolani Colon ◽  
Rishabh Hirday ◽  
Ami Patel ◽  
Amrita Poddar ◽  
Emma Tuberty-Vaughan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Outer Segment ◽  
Gene Discovery ◽  
Immunohistochemical Analysis ◽  
Transcriptome Profiling ◽  
Photoreceptor Cells ◽  
Functional Gene ◽  
Mouse Retina ◽  
Computational Pipeline ◽  
Photoreceptor Outer Segment

Abstract Many computational pipelines exist for the detection of differentially expressed genes. However, computational pipelines for functional gene detection are rarely exist. We developed a new computational pipeline for functional gene identification from transcriptome profiling data. Key features of the pipeline include clustering optimization by gap statistics, gene ontology analysis for each cluster, and literature analysis for functional gene discovery. By leveraging this pipeline on RNA-seq datasets of mouse retinal development studies, we identified 14 candidate genes involved in the formation of the photoreceptor outer segment. The expression of top three candidate genes (Pde8b, Laptm4b, and Nr1h4) in the outer segment of the developing mouse retina were experimentally validated by immunohistochemical analysis. This computational pipeline can accurately predict novel functional gene for a specific biological process, e.g., the outer segment development of the photoreceptor cells in the mouse retina. This pipeline is also applicable to functional gene discovery for any other biological processes and in any other organs and tissues.

scholarly journals PCARE and WASF3 regulate ciliary F-actin assembly that is required for the initiation of photoreceptor outer segment disk formation

2020 ◽  
Vol 117 (18) ◽  
pp. 9922-9931 ◽  
Author(s):  
Julio C. Corral-Serrano ◽  
Ideke J. C. Lamers ◽  
Jeroen van Reeuwijk ◽  
Lonneke Duijkers ◽  
Anita D. M. Hoogendoorn ◽  
...  
Keyword(s):  
Outer Segment ◽  
Actin Polymerization ◽  
Retinal Dystrophy ◽  
Photoreceptor Cells ◽  
Actin Dynamics ◽  
Mouse Retina ◽  
Specific Gene ◽  
Common Denominator ◽  
Photoreceptor Outer Segment ◽  
Disk Formation

The outer segments (OS) of rod and cone photoreceptor cells are specialized sensory cilia that contain hundreds of opsin-loaded stacked membrane disks that enable phototransduction. The biogenesis of these disks is initiated at the OS base, but the driving force has been debated. Here, we studied the function of the protein encoded by the photoreceptor-specific gene C2orf71, which is mutated in inherited retinal dystrophy (RP54). We demonstrate that C2orf71/PCARE (photoreceptor cilium actin regulator) can interact with the Arp2/3 complex activator WASF3, and efficiently recruits it to the primary cilium. Ectopic coexpression of PCARE and WASF3 in ciliated cells results in the remarkable expansion of the ciliary tip. This process was disrupted by small interfering RNA (siRNA)-based down-regulation of an actin regulator, by pharmacological inhibition of actin polymerization, and by the expression of PCARE harboring a retinal dystrophy-associated missense mutation. Using human retinal organoids and mouse retina, we observed that a similar actin dynamics-driven process is operational at the base of the photoreceptor OS where the PCARE module and actin colocalize, but which is abrogated in Pcare−/− mice. The observation that several proteins involved in retinal ciliopathies are translocated to these expansions renders it a potential common denominator in the pathomechanisms of these hereditary disorders. Together, our work suggests that PCARE is an actin-associated protein that interacts with WASF3 to regulate the actin-driven expansion of the ciliary membrane at the initiation of new outer segment disk formation.

PRCD is Concentrated at the Base of Photoreceptor Outer Segments and is Involved in Outer Segment Disc Formation

2019 ◽  
Author(s):  
Gilad Allon ◽  
Irit Mann ◽  
Lital Remez ◽  
Elisabeth Sehn ◽  
Leah Rizel ◽  
...  
Keyword(s):  
Retinal Degeneration ◽  
Knockout Mice ◽  
Outer Segment ◽  
Mouse Retina ◽  
Cone Photoreceptors ◽  
Photoreceptor Outer Segment ◽  
Photoreceptor Outer Segments ◽  
Outer Segments ◽  
Rod And Cone Photoreceptors ◽  
Disc Formation

Abstract Mutations of the PRCD gene are associated with rod-cone degeneration in both dogs and humans. Prcd is expressed in the mouse eye as early as embryonic day 14. In the adult mouse retina PRCD is expressed in the outer segments of both rod and cone photoreceptors. Immunoelectron microscopy revealed that PRCD is located at the outer segment rim, and that it is highly concentrated at the base of the outer segment. Prcd-knockout mice present with progressive retinal degeneration, starting at 20 weeks of age and onwards. This process is reflected by a significant and progressive reduction of both scotopic and photopic electroretinographic responses, and by thinning of the retina, and specifically of the outer nuclear layer, indicating photoreceptor loss. Electron microscopy revealed severe damage to photoreceptor outer segments, which is associated with immigration of microglia cells to the Prcd-knockout retina, and accumulation of vesicles in the inter-photoreceptor space. Phagocytosis of photoreceptor outer segment discs by the retinal pigmented epithelium is severely reduced. Our data show that Prcd-knockout mice serve as a good model for retinal degeneration caused by PRCD mutations in humans. Our findings in these mice support the involvement of PRCD in outer segment disc formation of both rod and cone photoreceptors. Furthermore, they suggest a feedback mechanism which coordinates the rate of photoreceptor outer segment disc formation, shedding and phagocytosis. This study has important implications for understanding the function of PRCD in the retina, as well as for future development of treatment modalities for PRCD-deficiency in humans.

scholarly journals KINETICS OF ROD OUTER SEGMENT RENEWAL IN THE DEVELOPING MOUSE RETINA

1973 ◽  
Vol 58 (3) ◽  
pp. 650-661 ◽  
Author(s):  
Matthew M. LaVail
Keyword(s):  
Outer Segment ◽  
Photoreceptor Cells ◽  
Mouse Retina ◽  
Rod Photoreceptor ◽  
Adult Level ◽  
Rod Outer Segment ◽  
Equilibrium Length ◽  
Kinetics Of ◽  
Late Stages ◽  
Adult Rate

The kinetics of rod outer segment renewal in the developing retina have been investigated in C57BL/6J mice. Litters of mice were injected with [3H]amino acids at various ages and killed at progressively later time intervals. Plastic 1.5 µm sections of retina were studied by light microscope autoradiography. The rate of outer segment disk synthesis, as judged by labeled disk displacement away from the site of synthesis, is slightly greater than the adult level at 11–13 days of age; it rises to more than 1.6 times the adult rate between days 13 and 17, after which it falls to the adult level at 21–25 days. The rate of disk disposal, as measured by labeled disk movement toward the site of disposal, is less than 15% of the adult level at 11–13 days of age; it rises sharply to almost 70% of the adult level by days 13–15 and then more gradually approaches the adult rate. The net difference in rates of synthesis and disposal accounts for the rapid elongation of rod outer segments in the mouse between days 11 and 17 and the subsequent, more gradual elongation to the adult equilibrium length reached between days 19 and 25. The changing rate of outer segment disk synthesis characterizes the late stages of cytodifferentiation of the rod photoreceptor cells.

scholarly journals Photoreceptor discs form through peripherin-dependent suppression of ciliary ectosome release

2017 ◽  
Vol 216 (5) ◽  
pp. 1489-1499 ◽  
Author(s):  
Raquel Y. Salinas ◽  
Jillian N. Pearring ◽  
Jin-Dong Ding ◽  
William J. Spencer ◽  
Ying Hao ◽  
...  
Keyword(s):  
Primary Cilium ◽  
Outer Segment ◽  
Genetic Material ◽  
Photoreceptor Cells ◽  
Specific Protein ◽  
Photoreceptor Outer Segment ◽  
Extracellular Signals ◽  
Membrane Surfaces ◽  
Light Capture ◽  
Innate Ability

The primary cilium is a highly conserved organelle housing specialized molecules responsible for receiving and processing extracellular signals. A recently discovered property shared across many cilia is the ability to release small vesicles called ectosomes, which are used for exchanging protein and genetic material among cells. In this study, we report a novel role for ciliary ectosomes in building the elaborate photoreceptor outer segment filled with hundreds of tightly packed “disc” membranes. We demonstrate that the photoreceptor cilium has an innate ability to release massive amounts of ectosomes. However, this process is suppressed by the disc-specific protein peripherin, which enables retained ectosomes to be morphed into discs. This new function of peripherin is performed independently from its well-established role in maintaining the high curvature of disc edges, and each function is fulfilled by a separate part of peripherin’s molecule. Our findings explain how the outer segment structure evolved from the primary cilium to provide photoreceptor cells with vast membrane surfaces for efficient light capture.

scholarly journals Distribution of guanylate cyclase within photoreceptor outer segments

1996 ◽  
Vol 109 (7) ◽  
pp. 1803-1812
Author(s):  
M.A. Hallett ◽  
J.L. Delaat ◽  
K. Arikawa ◽  
C.L. Schlamp ◽  
F. Kong ◽  
...  
Keyword(s):  
Guanylate Cyclase ◽  
Actin Filaments ◽  
Outer Segment ◽  
Essential Role ◽  
Photoreceptor Cells ◽  
Rod Photoreceptor ◽  
Light Activation ◽  
Photoreceptor Outer Segment ◽  
Photoreceptor Outer Segments ◽  
Vertebrate Photoreceptor

Guanylate cyclases play an essential role in the recovery of vertebrate photoreceptor cells after light activation. Here, we have investigated how one such guanylate cyclase, RetGC-1, is distributed within light- and dark-adapted rod photoreceptor cells. Guanylate cyclase activity partitioned with the photoreceptor outer segment (OS) cytoskeleton in a light-sensitive manner. RetGC-1 was found to bind actin filaments in actin blot overlays, suggesting a mechanism for its association with the OS cytoskeleton. In retinal sections, this enzyme was immunodetected only in the OSs, where it appeared to be distributed throughout the disk membranes.

scholarly journals Accumulation of non-outer segment proteins in the outer segment underlies photoreceptor degeneration in Bardet–Biedl syndrome

2015 ◽  
Vol 112 (32) ◽  
pp. E4400-E4409 ◽  
Author(s):  
Poppy Datta ◽  
Chantal Allamargot ◽  
Joseph S. Hudson ◽  
Emily K. Andersen ◽  
Sajag Bhattarai ◽  
...  
Keyword(s):  
Protein Trafficking ◽  
Outer Segment ◽  
Primary Cilia ◽  
Leucine Zipper ◽  
Photoreceptor Cells ◽  
Photoreceptor Degeneration ◽  
Photoreceptor Outer Segment ◽  
Bardet Biedl Syndrome ◽  
Major Function ◽  
Underlying Mechanisms

Compartmentalization and polarized protein trafficking are essential for many cellular functions. The photoreceptor outer segment (OS) is a sensory compartment specialized for phototransduction, and it shares many features with primary cilia. As expected, mutations disrupting protein trafficking to cilia often disrupt protein trafficking to the OS and cause photoreceptor degeneration. Bardet–Biedl syndrome (BBS) is one of the ciliopathies associated with defective ciliary trafficking and photoreceptor degeneration. However, precise roles of BBS proteins in photoreceptor cells and the underlying mechanisms of photoreceptor degeneration in BBS are not well understood. Here, we show that accumulation of non-OS proteins in the OS underlies photoreceptor degeneration in BBS. Using a newly developed BBS mouse model [Leucine zipper transcription factor-like 1 (Lztfl1)/Bbs17 mutant], isolated OSs, and quantitative proteomics, we determined 138 proteins that are enriched more than threefold in BBS mutant OS. In contrast, only eight proteins showed a more than threefold reduction. We found striking accumulation of Stx3 and Stxbp1/Munc18-1 and loss of polarized localization of Prom1 within the Lztfl1 and Bbs1 mutant OS. Ultrastructural analysis revealed that large vesicles are formed in the BBS OS, disrupting the lamellar structure of the OS. Our findings suggest that accumulation (and consequent sequestration) of non-OS proteins in the OS is likely the primary cause of photoreceptor degeneration in BBS. Our data also suggest that a major function of BBS proteins in photoreceptors is to transport proteins from the OS to the cell body or to prevent entry of non-OS proteins into the OS.

scholarly journals Light-dependent photoreceptor orientation in mouse retina

2020 ◽  
Vol 6 (51) ◽  
pp. eabe2782
Author(s):  
Zuying Chai ◽  
Daniel Silverman ◽  
Guang Li ◽  
David Williams ◽  
Elio Raviola ◽  
...  
Keyword(s):  
Early Life ◽  
Critical Period ◽  
Outer Segment ◽  
Mouse Retina ◽  
Photoreceptor Outer Segment ◽  
Human Eye ◽  
Rods And Cones ◽  
Pupil Center ◽  
Adult Mice

Almost a century ago, Stiles and Crawford reported that the human eye is more sensitive to light entering through the pupil center than through its periphery (Stiles-Crawford effect). This psychophysical phenomenon, later found to correlate with photoreceptor orientation toward the pupil, was dynamically phototropic, adjustable within days to an eccentrically displaced pupil. For decades, this phototropism has been speculated to involve coordinated movements of the rectilinear photoreceptor outer and inner segments. We report here that, unexpectedly, the murine photoreceptor outer segment has a seemingly light-independent orientation, but the inner segment’s orientation undergoes light-dependent movement, giving rise to nonrectilinear outer and inner segments in adult mice born and reared in darkness. Light during an early critical period (~P0 to P8), however, largely sets the correct photoreceptor orientation permanently afterward. Unexpectedly, abolishing rod and cone phototransductions did not mimic darkness in early life, suggesting photosignaling extrinsic to rods and cones is involved.

scholarly journals IFT20 is required for opsin trafficking and photoreceptor outer segment development

2011 ◽  
Vol 22 (7) ◽  
pp. 921-930 ◽  
Author(s):  
Brian T. Keady ◽  
Yun Zheng Le ◽  
Gregory J. Pazour
Keyword(s):  
Cell Body ◽  
Golgi Complex ◽  
Outer Segment ◽  
Intraflagellar Transport ◽  
Photoreceptor Cells ◽  
High Rate ◽  
Cell Degeneration ◽  
Photoreceptor Outer Segment ◽  
Rods And Cones ◽  
Cone Development

The light-detecting outer segments of vertebrate photoreceptors are cilia. Like other cilia, all materials needed for assembly and maintenance are synthesized in the cell body and transported into the cilium. The highly elaborated nature of the outer segment and its high rate of turnover necessitate unusually high levels of transport into the cilium. In this work, we examine the role of the IFT20 subunit of the intraflagellar transport (IFT) particle in photoreceptor cells. IFT20 was deleted in developing cones by a cone-specific Cre and in mature rods and cones by a tamoxifen-activatable Cre. Loss of IFT20 during cone development leads to opsin accumulation in the inner segment even when the connecting cilium and outer segment are still intact. With time this causes cone cell degeneration. Similarly, deletion of IFT20 in mature rods causes rapid accumulation of rhodopsin in the cell body, where it is concentrated at the Golgi complex. We further show that IFT20, acting both as part of the IFT particle and independent of the particle, binds to rhodopsin and RG-opsin. Since IFT20 dynamically moves between the Golgi complex and the connecting cilium, the current work suggests that rhodopsin and opsins are cargo for IFT transport.

scholarly journals Localization of Usher 1 proteins to the photoreceptor calyceal processes, which are absent from mice

2012 ◽  
Vol 199 (2) ◽  
pp. 381-399 ◽  
Author(s):  
Iman Sahly ◽  
Eric Dufour ◽  
Cataldo Schietroma ◽  
Vincent Michel ◽  
Amel Bahloul ◽  
...  
Keyword(s):  
Retinal Degeneration ◽  
Outer Segment ◽  
Usher Syndrome ◽  
Retinal Dystrophy ◽  
Photoreceptor Cells ◽  
Type I ◽  
Photoreceptor Outer Segment ◽  
Membrane Interfaces ◽  
Protocadherin 15 ◽  
Cadherin 23

The mechanisms underlying retinal dystrophy in Usher syndrome type I (USH1) remain unknown because mutant mice lacking any of the USH1 proteins—myosin VIIa, harmonin, cadherin-23, protocadherin-15, sans—do not display retinal degeneration. We found here that, in macaque photoreceptor cells, all USH1 proteins colocalized at membrane interfaces (i) between the inner and outer segments in rods and (ii) between the microvillus-like calyceal processes and the outer segment basolateral region in rods and cones. This pattern, conserved in humans and frogs, was mediated by the formation of an USH1 protein network, which was associated with the calyceal processes from the early embryonic stages of outer segment growth onwards. By contrast, mouse photoreceptors lacked calyceal processes and had no USH1 proteins at the inner–outer segment interface. We suggest that USH1 proteins form an adhesion belt around the basolateral region of the photoreceptor outer segment in humans, and that defects in this structure cause the retinal degeneration in USH1 patients.

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