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Li Z, Klein JA, Rampam S, Kurzion R, Campbell NB, Patel Y, Haydar TF, Zeldich E. Asynchronous excitatory neuron development in an isogenic cortical spheroid model of Down syndrome. Front Neurosci 2022; 16:932384. [PMID: 36161168 PMCID: PMC9504873 DOI: 10.3389/fnins.2022.932384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022] Open
Abstract
The intellectual disability (ID) in Down syndrome (DS) is thought to result from a variety of developmental deficits such as alterations in neural progenitor division, neurogenesis, gliogenesis, cortical architecture, and reduced cortical volume. However, the molecular processes underlying these neurodevelopmental changes are still elusive, preventing an understanding of the mechanistic basis of ID in DS. In this study, we used a pair of isogenic (trisomic and euploid) induced pluripotent stem cell (iPSC) lines to generate cortical spheroids (CS) that model the impact of trisomy 21 on brain development. Cortical spheroids contain neurons, astrocytes, and oligodendrocytes and they are widely used to approximate early neurodevelopment. Using single cell RNA sequencing (scRNA-seq), we uncovered cell type-specific transcriptomic changes in the trisomic CS. In particular, we found that excitatory neuron populations were most affected and that a specific population of cells with a transcriptomic profile resembling layer IV cortical neurons displayed the most profound divergence in developmental trajectory between trisomic and euploid genotypes. We also identified candidate genes potentially driving the developmental asynchrony between trisomic and euploid excitatory neurons. Direct comparison between the current isogenic CS scRNA-seq data and previously published datasets revealed several recurring differentially expressed genes between DS and control samples. Altogether, our study highlights the power and importance of cell type-specific analyses within a defined genetic background, coupled with broader examination of mixed samples, to comprehensively evaluate cellular phenotypes in the context of DS.
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Affiliation(s)
- Zhen Li
- Center for Neuroscience Research, Children’s National Hospital, Washington, DC, United States
| | - Jenny A. Klein
- Center for Neuroscience Research, Children’s National Hospital, Washington, DC, United States
- Graduate Program for Neuroscience, Boston University, Boston, MA, United States
| | - Sanjeev Rampam
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Ronni Kurzion
- Department of Chemistry, Boston University, Boston, MA, United States
| | | | - Yesha Patel
- Department of Anatomy and Neurobiology, Boston University, Boston, MA, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Tarik F. Haydar
- Center for Neuroscience Research, Children’s National Hospital, Washington, DC, United States
| | - Ella Zeldich
- Department of Anatomy and Neurobiology, Boston University, Boston, MA, United States
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Zhang J, Choi EH, Tworak A, Salom D, Leinonen H, Sander CL, Hoang TV, Handa JT, Blackshaw S, Palczewska G, Kiser PD, Palczewski K. Photic generation of 11- cis-retinal in bovine retinal pigment epithelium. J Biol Chem 2019; 294:19137-19154. [PMID: 31694912 DOI: 10.1074/jbc.ra119.011169] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/25/2019] [Indexed: 12/19/2022] Open
Abstract
Photoisomerization of the 11-cis-retinal chromophore of rod and cone visual pigments to an all-trans-configuration is the initiating event for vision in vertebrates. The regeneration of 11-cis-retinal, necessary for sustained visual function, is an endergonic process normally conducted by specialized enzyme systems. However, 11-cis-retinal also can be formed through reverse photoisomerization from all-trans-retinal. A nonvisual opsin known as retinal pigment epithelium (RPE)-retinal G-protein-coupled receptor (RGR) was previously shown to mediate visual chromophore regeneration in photic conditions, but conflicting results have cast doubt on its role as a photoisomerase. Here, we describe high-level production of 11-cis-retinal from RPE membranes stimulated by illumination at a narrow band of wavelengths. This activity was associated with RGR and enhanced by cellular retinaldehyde-binding protein (CRALBP), which binds the 11-cis-retinal produced by RGR and prevents its re-isomerization to all-trans-retinal. The activity was recapitulated with cells heterologously expressing RGR and with purified recombinant RGR. Using an RGR variant, K255A, we confirmed that a Schiff base linkage at Lys-255 is critical for substrate binding and isomerization. Single-cell RNA-Seq analysis of the retina and RPE tissue confirmed that RGR is expressed in human and bovine RPE and Müller glia, whereas mouse RGR is expressed in RPE but not in Müller glia. These results provide key insights into the mechanisms of physiological retinoid photoisomerization and suggest a novel mechanism by which RGR, in concert with CRALBP, regenerates the visual chromophore in the RPE under sustained light conditions.
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Affiliation(s)
- Jianye Zhang
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697
| | - Elliot H Choi
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697.,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Aleksander Tworak
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697
| | - David Salom
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697
| | - Henri Leinonen
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697
| | - Christopher L Sander
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697.,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Thanh V Hoang
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - James T Handa
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.,Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | | | - Philip D Kiser
- Department of Physiology and Biophysics, University of California, Irvine, California 92697.,Research Service, Veterans Affairs Long Beach Healthcare System, Long Beach, California 90822
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697
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Hartin SN, Hudson ML, Yingling C, Ackley BD. A Synthetic Lethal Screen Identifies a Role for Lin-44/Wnt in C. elegans Embryogenesis. PLoS One 2015; 10:e0121397. [PMID: 25938228 PMCID: PMC4418752 DOI: 10.1371/journal.pone.0121397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/31/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The C. elegans proteins PTP-3/LAR-RPTP and SDN-1/Syndecan are conserved cell adhesion molecules. Loss-of-function (LOF) mutations in either ptp-3 or sdn-1 result in low penetrance embryonic developmental defects. Work from other systems has shown that syndecans can function as ligands for LAR receptors in vivo. We used double mutant analysis to test whether ptp-3 and sdn-1 function in a linear genetic pathway during C. elegans embryogenesis. RESULTS We found animals with LOF in both sdn-1 and ptp-3 exhibited a highly penetrant synthetic lethality (SynLet), with only a small percentage of animals surviving to adulthood. Analysis of the survivors demonstrated that these animals had a synergistic increase in the penetrance of embryonic developmental defects. Together, these data strongly suggested PTP-3 and SDN-1 function in parallel during embryogenesis. We subsequently used RNAi to knockdown ~3,600 genes predicted to encode secreted and/or transmembrane molecules to identify genes that interacted with ptp-3 or sdn-1. We found that the Wnt ligand, lin-44, was SynLet with sdn-1, but not ptp-3. We used 4-dimensional time-lapse analysis to characterize the interaction between lin-44 and sdn-1. We found evidence that loss of lin-44 caused defects in the polarization and migration of endodermal precursors during gastrulation, a previously undescribed role for lin-44 that is strongly enhanced by the loss of sdn-1. CONCLUSIONS PTP-3 and SDN-1 function in compensatory pathways during C. elegans embryonic and larval development, as simultaneous loss of both genes has dire consequences for organismal survival. The Wnt ligand lin-44 contributes to the early stages of gastrulation in parallel to sdn-1, but in a genetic pathway with ptp-3. Overall, the SynLet phenotype provides a robust platform to identify ptp-3 and sdn-1 interacting genes, as well as other genes that function in development, yet might be missed in traditional forward genetic screens.
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Affiliation(s)
- Samantha N. Hartin
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States of America
| | - Martin L. Hudson
- Department of Biology and Physics, Kennesaw State University, Kennesaw, GA, United States of America
| | - Curtis Yingling
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States of America
| | - Brian D. Ackley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States of America
- * E-mail:
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Craig SEL, Brady-Kalnay SM. Regulation of development and cancer by the R2B subfamily of RPTPs and the implications of proteolysis. Semin Cell Dev Biol 2014; 37:108-18. [PMID: 25223585 DOI: 10.1016/j.semcdb.2014.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/04/2014] [Accepted: 09/05/2014] [Indexed: 01/04/2023]
Abstract
The initial cloning of receptor protein tyrosine phosphatases (RPTPs) was met with excitement because of their hypothesized function in counterbalancing receptor tyrosine kinase signaling. In recent years, members of a subfamily of RPTPs with homophilic cell-cell adhesion capabilities, known as the R2B subfamily, have been shown to have functions beyond that of counteracting tyrosine kinase activity, by independently influencing cell signaling in their own right and by regulating cell adhesion. The R2B subfamily is composed of four members: PTPmu (PTPRM), PTPrho (PTPRT), PTPkappa (PTPRK), and PCP-2 (PTPRU). The effects of this small subfamily of RPTPs is far reaching, influencing several developmental processes and cancer. In fact, R2B RPTPs are predicted to be tumor suppressors and are among the most frequently mutated protein tyrosine phosphatases (PTPs) in cancer. Confounding these conclusions are more recent studies suggesting that proteolysis of the full-length R2B RPTPs result in oncogenic extracellular and intracellular protein fragments. This review discusses the current knowledge of the role of R2B RPTPs in development and cancer, with special detail given to the mechanisms and implications that proteolysis has on R2B RPTP function. We also touch upon the concept of exploiting R2B proteolysis to develop cancer imaging tools, and consider the effects of R2B proteolysis on axon guidance, perineural invasion and collective cell migration.
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Affiliation(s)
- Sonya E L Craig
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4960, USA
| | - Susann M Brady-Kalnay
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4960, USA; Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
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Receptor protein tyrosine phosphatases are expressed by cycling retinal progenitor cells and involved in neuronal development of mouse retina. Neuroscience 2008; 152:618-45. [DOI: 10.1016/j.neuroscience.2008.01.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 12/14/2007] [Accepted: 01/10/2008] [Indexed: 11/21/2022]
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Asano A, Tsubomatsu K, Jung CG, Sasaki N, Agui T. A deletion mutation of the protein tyrosine phosphatase kappa (Ptprk) gene is responsible for T-helper immunodeficiency (thid) in the LEC rat. Mamm Genome 2007; 18:779-86. [PMID: 17909891 DOI: 10.1007/s00335-007-9062-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 08/13/2007] [Indexed: 11/24/2022]
Abstract
Bone marrow (BM)-derived T-cell progenitors differentiate into CD4 or CD8 single-positive (SP) cells in the thymus. We have previously reported that a single autosomal mutation, thid, causes a defect in the maturation of CD4 SP thymocytes and an abnormality of peripheral helper T cells in the LEC rat. In this study we attempted to identify a gene responsible for the thid mutation. We first performed genetic linkage analysis and mapped the thid locus between Myb and D1Rat392 on Chr 1. In this region we found an approximately 380-kb deletion from intron 3 of the Ptprk gene, which encodes a receptor-like protein tyrosine phosphatase type kappa (RPTPkappa) to intron 1 of the RGD1560849 predicted gene in the LEC rat genome. Reconstitution with syngenic BM cells transduced Ptprk but not the RGD1560849 predicted gene rescued development of CD4 SP cells in the LEC rat thymus. It is confirmed by this result that the Ptprk gene is responsible for the thid mutation in the LEC rat. Our results further suggest that RPTPkappa plays a critical role in the development of CD4 SP cells in the thymus.
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Affiliation(s)
- Atsushi Asano
- Laboratory of Experimental Animal Science, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
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Eswaran J, Debreczeni JE, Longman E, Barr AJ, Knapp S. The crystal structure of human receptor protein tyrosine phosphatase kappa phosphatase domain 1. Protein Sci 2006; 15:1500-5. [PMID: 16672235 PMCID: PMC2242534 DOI: 10.1110/ps.062128706] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The receptor-type protein tyrosine phosphatases (RPTPs) are integral membrane proteins composed of extracellular adhesion molecule-like domains, a single transmembrane domain, and a cytoplasmic domain. The cytoplasmic domain consists of tandem PTP domains, of which the D1 domain is enzymatically active. RPTPkappa is a member of the R2A/IIb subfamily of RPTPs along with RPTPmu, RPTPrho, and RPTPlambda. Here, we have determined the crystal structure of catalytically active, monomeric D1 domain of RPTPkappa at 1.9 A. Structural comparison with other PTP family members indicates an overall classical PTP architecture of twisted mixed beta-sheets flanked by alpha-helices, in which the catalytically important WPD loop is in an unhindered open conformation. Though the residues forming the dimeric interface in the RPTPmu structure are all conserved, they are not involved in the protein-protein interaction in RPTPkappa. The N-terminal beta-strand, formed by betax association with betay, is conserved only in RPTPs but not in cytosolic PTPs, and this feature is conserved in the RPTPkappa structure forming a beta-strand. Analytical ultracentrifugation studies show that the presence of reducing agents and higher ionic strength are necessary to maintain RPTPkappa as a monomer. In this family the crystal structure of catalytically active RPTPmu D1 was solved as a dimer, but the dimerization was proposed to be a consequence of crystallization since the protein was monomeric in solution. In agreement, we show that RPTPkappa is monomeric in solution and crystal structure.
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Affiliation(s)
- Jeyanthy Eswaran
- Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, United Kingdom
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Hantman AW, Perl ER. Molecular and genetic features of a labeled class of spinal substantia gelatinosa neurons in a transgenic mouse. J Comp Neurol 2006; 492:90-100. [PMID: 16175558 DOI: 10.1002/cne.20709] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genetic incorporation in a mouse of a transgene containing the prion promoter and the green fluorescent protein (GFP) coding sequence labels a set of substantia gelatinosa (SG) neurons (SG-GFP) homogenous in morphology, electrophysiology, and gamma-amino-butyric acid expression. In the present analysis the SG-GFP neurons are established to have protein kinase C-betaII immunoreactivity and to lack evidence for the presence of calbindin D-28k, parvalbumin, and protein kinase C-gamma. These neurons were hyperpolarized by mediators of descending control, norepinephrine and serotonin. Sequential polymerase chain reactions established the insertion of the transgene to be in the receptor protein tyrosine phosphatase kappa (RPTP-kappa) and the laminin receptor 1 (ribosomal protein SA) pseudogene 1 locus. RPTP-kappa expression in both GFP-labeled dorsal root ganglia and SG neurons raises the possibility that homophilic interactions of RPTP-kappa contribute to establishment of connections between specific classes of primary afferent and SG neurons.
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Affiliation(s)
- Adam W Hantman
- Department of Cell and Molecular Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Ensslen-Craig SE, Brady-Kalnay SM. Receptor protein tyrosine phosphatases regulate neural development and axon guidance. Dev Biol 2004; 275:12-22. [PMID: 15464569 DOI: 10.1016/j.ydbio.2004.08.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Revised: 08/05/2004] [Accepted: 08/08/2004] [Indexed: 01/06/2023]
Abstract
The regulation of tyrosine phosphorylation is recognized as an important developmental mechanism. Both addition and removal of phosphate moieties on tyrosine residues are tightly regulated during development. Originally, most attention focused on the role of tyrosine kinases during development, but more recently, the developmental importance of tyrosine phosphatases has been gaining interest. Receptor protein tyrosine phosphatases (RPTPs) are of particular interest to developmental biologists because the extracellular domains of RPTPs are similar to those of cell adhesion molecules (CAMs). This suggests that RPTPs may have functions in development similar to CAMs. This review focuses on the role of RPTPs in development of the nervous system in processes such as axon guidance, synapse formation, and neural tissue morphogenesis.
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Affiliation(s)
- Sonya E Ensslen-Craig
- Department of Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, OH 44106-4960, USA
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