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Shiels A. Through the Cat-Map Gateway: A Brief History of Cataract Genetics. Genes (Basel) 2024; 15:785. [PMID: 38927721 PMCID: PMC11202810 DOI: 10.3390/genes15060785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Clouding of the transparent eye lens, or cataract(s), is a leading cause of visual impairment that requires surgical replacement with a synthetic intraocular lens to effectively restore clear vision. Most frequently, cataract is acquired with aging as a multifactorial or complex trait. Cataract may also be inherited as a classic Mendelian trait-often with an early or pediatric onset-with or without other ocular and/or systemic features. Since the early 1990s, over 85 genes and loci have been genetically associated with inherited and/or age-related forms of cataract. While many of these underlying genes-including those for lens crystallins, connexins, and transcription factors-recapitulate signature features of lens development and differentiation, an increasing cohort of unpredicted genes, including those involved in cell-signaling, membrane remodeling, and autophagy, has emerged-providing new insights regarding lens homeostasis and aging. This review provides a brief history of gene discovery for inherited and age-related forms of cataract compiled in the Cat-Map database and highlights potential gene-based therapeutic approaches to delay, reverse, or even prevent cataract formation that may help to reduce the increasing demand for cataract surgery.
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Affiliation(s)
- Alan Shiels
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
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2
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Zhang L, Liu X, Li W, Liu K, Zhang J, Liu X, Wang J. Integrative transcriptomic profiling of ncRNAs and mRNAs in developing mouse lens. Front Genet 2024; 15:1405715. [PMID: 38933921 PMCID: PMC11199715 DOI: 10.3389/fgene.2024.1405715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
In recent years, burgeoning research has underscored the pivotal role of non-coding RNA in orchestrating the growth, development, and pathogenesis of various diseases across organisms. However, despite these advances, our understanding of the specific contributions of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) to lens development remains notably limited. Clarifying the intricate gene regulatory networks is imperative for unraveling the molecular underpinnings of lens-related disorders. In this study, we aimed to address this gap by conducting a comprehensive analysis of the expression profiles of messenger RNAs (mRNAs), lncRNAs, and circRNAs at critical developmental time points of the mouse lens, encompassing both embryonic (E10.5, E12.5, and E16.5) and postnatal stages (P0.5, P10.5, and P60). Leveraging RNA-sequencing technology, we identified key transcripts pivotal to lens development. Our analysis revealed differentially expressed (DE) mRNAs, lncRNAs, and circRNAs across various developmental stages. Particularly noteworthy, there were 1831 co-differentially expressed (CO-DE) mRNAs, 150 CO-DE lncRNAs, and 13 CO-DE circRNAs identified during embryonic stages. Gene Ontology (GO) enrichment analysis unveiled associations primarily related to lens development, DNA conformational changes, and angiogenesis among DE mRNAs and lncRNAs. Furthermore, employing protein-protein interaction networks, mRNA-lncRNA co-expression networks, and circRNA-microRNA-mRNA networks, we predicted candidate key molecules implicated in lens development. Our findings underscore the pivotal roles of lncRNAs and circRNAs in this process, offering fresh insights into the pathogenesis of lens-related disorders and paving the way for future exploration in this field.
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Affiliation(s)
- Liyun Zhang
- Department of Ophthalmology, General Hospital of Central Theater Command, Wuhan, China
| | - Xin Liu
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| | - Wei Li
- Department of Pediatric Respiratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kaiqing Liu
- The Department of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Jing Zhang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| | - Xinhua Liu
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| | - Jiantao Wang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
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3
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Shah R, Amador C, Chun ST, Ghiam S, Saghizadeh M, Kramerov AA, Ljubimov AV. Non-canonical Wnt signaling in the eye. Prog Retin Eye Res 2023; 95:101149. [PMID: 36443219 PMCID: PMC10209355 DOI: 10.1016/j.preteyeres.2022.101149] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
Wnt signaling comprises a group of complex signal transduction pathways that play critical roles in cell proliferation, differentiation, and apoptosis during development, as well as in stem cell maintenance and adult tissue homeostasis. Wnt pathways are classified into two major groups, canonical (β-catenin-dependent) or non-canonical (β-catenin-independent). Most previous studies in the eye have focused on canonical Wnt signaling, and the role of non-canonical signaling remains poorly understood. Additionally, the crosstalk between canonical and non-canonical Wnt signaling in the eye has hardly been explored. In this review, we present an overview of available data on ocular non-canonical Wnt signaling, including developmental and functional aspects in different eye compartments. We also discuss important changes of this signaling in various ocular conditions, such as keratoconus, aniridia-related keratopathy, diabetes, age-related macular degeneration, optic nerve damage, pathological angiogenesis, and abnormalities in the trabecular meshwork and conjunctival cells, and limbal stem cell deficiency.
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Affiliation(s)
- Ruchi Shah
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cynthia Amador
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Steven T Chun
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA; University of California Los Angeles, Los Angeles, CA, USA
| | - Sean Ghiam
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Sackler School of Medicine, New York State/American Program of Tel Aviv University, Tel Aviv, Israel
| | - Mehrnoosh Saghizadeh
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Andrei A Kramerov
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alexander V Ljubimov
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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4
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Bileck A, Bortel P, Kriz M, Janker L, Kiss E, Gerner C, Del Favero G. Inward Outward Signaling in Ovarian Cancer: Morpho-Phospho-Proteomic Profiling Upon Application of Hypoxia and Shear Stress Characterizes the Adaptive Plasticity of OVCAR-3 and SKOV-3 Cells. Front Oncol 2022; 11:746411. [PMID: 35251951 PMCID: PMC8896345 DOI: 10.3389/fonc.2021.746411] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/27/2021] [Indexed: 12/26/2022] Open
Abstract
With the onset of resistance, ovarian cancer cells display almost unpredictable adaptive potential. This may derive from the tumor genetic ancestry and can be additionally tailored by post translational protein modifications (PTMs). In this study, we took advantage of high-end (phospho)-proteome analysis combined with multiparametric morphometric profiling in high-grade serous (OVCAR-3) and non-serous (SKOV-3) ovarian carcinoma cells. For functional experiments, we applied two different protocols, representing typical conditions of the abdominal cavity and of the growing tumor tissue: on the one side hypoxia (oxygen 1%) which develops within the tumor mass or is experienced during migration/extravasation in non-vascularized areas. On the other hand, fluid shear stress (250 rpm, 2.8 dyn/cm2) which affects tumor surface in the peritoneum or metastases in the bloodstream. After 3 hours incubation, treatment groups were clearly distinguishable by PCA analysis. Whereas basal proteome profiles of OVCAR-3 and SKOV-3 cells appeared almost unchanged, phosphoproteome analysis revealed multiple regulatory events. These affected primarily cellular structure and proliferative potential and consolidated in the proteome signature after 24h treatment. Upon oxygen reduction, metabolism switched toward glycolysis (e.g. upregulation hexokinase-2; HK2) and cell size increased, in concerted regulation of pathways related to Rho-GTPases and/or cytoskeletal elements, resembling a vasculogenic mimicry response. Shear stress regulated proteins governing cell cycle and structure, as well as the lipid metabolism machinery including the delta(14)-sterol reductase, kinesin-like proteins (KIF-22/20A) and the actin-related protein 2/3 complex. Independent microscopy-based validation experiments confirmed cell-type specific morphometric responses. In conclusion, we established a robust workflow enabling the description of the adaptive potential of ovarian cancer cells to physical and chemical stressors typical for the abdominal cavity and supporting the identification of novel molecular mechanisms sustaining tumor plasticity and pharmacologic resistance.
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Affiliation(s)
- Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Patricia Bortel
- Department of Analytical Chemistry, Faculty of Chemistry University of Vienna, Vienna, Austria
| | - Michelle Kriz
- Department of Analytical Chemistry, Faculty of Chemistry University of Vienna, Vienna, Austria
- Department of Food Chemistry and Toxicology, Faculty of Chemistry University of Vienna, Vienna, Austria
| | - Lukas Janker
- Department of Analytical Chemistry, Faculty of Chemistry University of Vienna, Vienna, Austria
| | - Endre Kiss
- Core Facility Multimodal Imaging, Faculty of Chemistry University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
- Core Facility Multimodal Imaging, Faculty of Chemistry University of Vienna, Vienna, Austria
- *Correspondence: Giorgia Del Favero, ; Christopher Gerner,
| | - Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry University of Vienna, Vienna, Austria
- Core Facility Multimodal Imaging, Faculty of Chemistry University of Vienna, Vienna, Austria
- *Correspondence: Giorgia Del Favero, ; Christopher Gerner,
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5
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Yang D, Zhou H, Lin J, Zhao S, Zhou H, Yin Z, Ni B, Chen Y, Xie W. Case Report: A Novel Missense Variant in the SIPA1L3 Gene Associated With Cataracts in a Chinese Family. Front Genet 2021; 12:715599. [PMID: 34603379 PMCID: PMC8481882 DOI: 10.3389/fgene.2021.715599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/19/2021] [Indexed: 11/23/2022] Open
Abstract
The signal-induced proliferation-associated 1-like 3 (SIPA1L3) gene that encodes a putative Rap GTPase-activating protein (RapGAP) has been associated with congenital cataract and eye development abnormalities. However, our current understanding of the mutation spectrum of SIPA1L3 associated with eye defects is limited. By using whole-exome sequencing plus Sanger sequencing validation, we identified a novel heterozygous c.1871A > G (p.Lys624Arg) variation within the predicted RapGAP domain of SIPA1L3 in the proband with isolated juvenile-onset cataracts from a three-generation Chinese family. In this family, the proband's father and grandmother were also heterozygous for the c.1871A > G variation and affected by cataracts varying in morphology, severity, and age of onset. Sequence alignment shows that the Lys 624 residue of SIPA1L3 is conserved across the species. Based on the resolved structure of Rap1–Rap1GAP complex, homology modeling implies that the Lys 624 residue is structurally homologous to the Lys 194 of Rap1GAP, a highly conserved lysine residue that is involved in the interface between Rap1 and Rap1GAP and critical for the affinity to Rap·GTP. We reasoned that arginine substitution of lysine 624 might have an impact on the SIPA1L3-Rap·GTP interaction, thereby affecting the regulatory function of SIPA1L3 on Rap signaling. Collectively, our finding expands the mutation spectrum of SIPA1L3 and provides new clues to the molecular mechanisms of SIPA1L3-related cataracts. Further investigations are warranted to validate the functional alteration of the p.Lys624Arg variant of SIPA1L3.
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Affiliation(s)
- Duo Yang
- Department of Ophthalmology, The Jili Hospital of Liuyang and the Eye Hospital of Liuyang, Changsha, China
| | - Haiyan Zhou
- National Health Committee Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jiwu Lin
- National Health Committee Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Shuangxi Zhao
- Department of Ophthalmology, The Jili Hospital of Liuyang and the Eye Hospital of Liuyang, Changsha, China
| | - Hao Zhou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhaochu Yin
- National Health Committee Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Bin Ni
- National Health Committee Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Yong Chen
- National Health Committee Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Wanqin Xie
- National Health Committee Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
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6
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Shiels A, Hejtmancik JF. Inherited cataracts: Genetic mechanisms and pathways new and old. Exp Eye Res 2021; 209:108662. [PMID: 34126080 PMCID: PMC8595562 DOI: 10.1016/j.exer.2021.108662] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/13/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022]
Abstract
Cataract(s) is the clinical equivalent of lens opacity and is caused by light scattering either by high molecular weight protein aggregates in lens cells or disruption of the lens microarchitecture itself. Genetic mutations underlying inherited cataract can provide insight into the biological processes and pathways critical for lens homeostasis and transparency, classically including the lens crystallins, connexins, membrane proteins or components, and intermediate filament proteins. More recently, cataract genes have been expanded to include newly identified biological processes such as chaperone or protein degradation components, transcription or growth factors, channels active in the lens circulation, and collagen and extracellular matrix components. Cataracts can be classified by age, and in general congenital cataracts are caused by severe mutations resulting in major damage to lens proteins, while age related cataracts are associated with variants that merely destabilize proteins thereby increasing susceptibility to environmental insults over time. Thus there might be separate pathways to opacity for congenital and age-related cataracts whereby congenital cataracts induce the unfolded protein response (UPR) and apoptosis to destroy the lens microarchitecture, while in age related cataract high molecular weight (HMW) aggregates formed by denatured crystallins bound by α-crystallin result in light scattering without severe damage to the lens microarchitecture.
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Affiliation(s)
- Alan Shiels
- Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892-1860, USA.
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7
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Harding P, Toms M, Schiff E, Owen N, Bell S, Lloyd IC, Moosajee M. EPHA2 Segregates with Microphthalmia and Congenital Cataracts in Two Unrelated Families. Int J Mol Sci 2021; 22:2190. [PMID: 33671840 PMCID: PMC7926380 DOI: 10.3390/ijms22042190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
EPHA2 is a transmembrane tyrosine kinase receptor that, when disrupted, causes congenital and age-related cataracts. Cat-Map reports 22 pathogenic EPHA2 variants associated with congenital cataracts, variable microcornea, and lenticonus, but no previous association with microphthalmia (small, underdeveloped eye, ≥2 standard deviations below normal axial length). Microphthalmia arises from ocular maldevelopment with >90 monogenic causes, and can include a complex ocular phenotype. In this paper, we report two pathogenic EPHA2 variants in unrelated families presenting with bilateral microphthalmia and congenital cataracts. Whole genome sequencing through the 100,000 Genomes Project and cataract-related targeted gene panel testing identified autosomal dominant heterozygous mutations segregating with the disease: (i) missense c.1751C>T, p.(Pro584Leu) and (ii) splice site c.2826-9G>A. To functionally validate pathogenicity, morpholino knockdown of epha2a/epha2b in zebrafish resulted in significantly reduced eye size ± cataract formation. Misexpression of N-cadherin and retained fibre cell nuclei were observed in the developing lens of the epha2b knockdown morphant fish by 3 days post-fertilisation, which indicated a putative mechanism for microphthalmia pathogenesis through disruption of cadherin-mediated adherens junctions, preventing lens maturation and the critical signals stimulating eye growth. This study demonstrates a novel association of EPHA2 with microphthalmia, suggesting further analysis of pathogenic variants in unsolved microphthalmia cohorts may increase molecular diagnostic rates.
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Affiliation(s)
- Philippa Harding
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (P.H.); (M.T.); (N.O.)
| | - Maria Toms
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (P.H.); (M.T.); (N.O.)
- The Francis Crick Institute, London NW1 1AT, UK
| | - Elena Schiff
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (E.S.); (S.B.)
| | - Nicholas Owen
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (P.H.); (M.T.); (N.O.)
| | - Suzannah Bell
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (E.S.); (S.B.)
| | - Ian Christopher Lloyd
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK;
- Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PT, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (P.H.); (M.T.); (N.O.)
- The Francis Crick Institute, London NW1 1AT, UK
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (E.S.); (S.B.)
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
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8
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Genome Editing of the SNAI1 Gene in Rhabdomyosarcoma: A Novel Model for Studies of Its Role. Cells 2020; 9:cells9051095. [PMID: 32354171 PMCID: PMC7290443 DOI: 10.3390/cells9051095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022] Open
Abstract
Genome editing (GE) tools and RNA interference technology enable the modulation of gene expression in cancer research. While GE mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 or transcription activator-like effector nucleases (TALEN) activity can be used to induce gene knockouts, shRNA interacts with the targeted transcript, resulting in gene knockdown. Here, we compare three different methods for SNAI1 knockout or knockdown in rhabdomyosarcoma (RMS) cells. RMS is the most common sarcoma in children and its development has been previously associated with SNAI1 transcription factor activity. To investigate the role of SNAI1 in RMS development, we compared CRISPR/Cas9, TALEN, and shRNA tools to identify the most efficient tool for the modulation of SNAI1 expression with biological effects. Subsequently, the genome sequence, transcript levels, and protein expression of SNAI1 were evaluated. The modulation of SNAI1 using three different approaches affected the morphology of the cells and modulated the expression of myogenic factors and HDAC1. Our study revealed a similar effectiveness of the tested methods. Nevertheless, the low efficiency of the GE tools was a limiting factor in obtaining biallelic gene knockouts. To conclude, we established and characterized three different models of SNAI1 knockout and knockdown that might be used in further studies investigating the role of SNAI1 in RMS.
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9
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Tao F, Beecham GW, Rebelo AP, Svaren J, Blanton SH, Moran JJ, Lopez-Anido C, Morrow JM, Abreu L, Rizzo D, Kirk CA, Wu X, Feely S, Verhamme C, Saporta MA, Herrmann DN, Day JW, Sumner CJ, Lloyd TE, Li J, Yum SW, Taroni F, Baas F, Choi BO, Pareyson D, Scherer SS, Reilly MM, Shy ME, Züchner S. Variation in SIPA1L2 is correlated with phenotype modification in Charcot- Marie- Tooth disease type 1A. Ann Neurol 2020; 85:316-330. [PMID: 30706531 DOI: 10.1002/ana.25426] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 01/28/2023]
Abstract
OBJECTIVE Genetic modifiers in rare disease have long been suspected to contribute to the considerable variance in disease expression, including Charcot-Marie-Tooth disease type 1A (CMT1A). To address this question, the Inherited Neuropathy Consortium collected a large standardized sample of such rare CMT1A patients over a period of 8 years. CMT1A is caused in most patients by a uniformly sized 1.5 Mb duplication event involving the gene PMP22. METHODS We genotyped DNA samples from 971 CMT1A patients on Illumina BeadChips. Genome-wide analysis was performed in a subset of 330 of these patients, who expressed the extremes of a hallmark symptom: mild and severe foot dorsiflexion strength impairment. SIPA1L2 (signal-induced proliferation-associated 1 like 2), the top identified candidate modifier gene, was expressed in the peripheral nerve, and our functional studies identified and confirmed interacting proteins using coimmunoprecipitation analysis, mass spectrometry, and immunocytochemistry. Chromatin immunoprecipitation and in vitro siRNA experiments were used to analyze gene regulation. RESULTS We identified significant association of 4 single nucleotide polymorphisms (rs10910527, rs7536385, rs4649265, rs1547740) in SIPA1L2 with foot dorsiflexion strength (p < 1 × 10-7 ). Coimmunoprecipitation and mass spectroscopy studies identified β-actin and MYH9 as SIPA1L2 binding partners. Furthermore, we show that SIPA1L2 is part of a myelination-associated coexpressed network regulated by the master transcription factor SOX10. Importantly, in vitro knockdown of SIPA1L2 in Schwannoma cells led to a significant reduction of PMP22 expression, hinting at a potential strategy for drug development. INTERPRETATION SIPA1L2 is a potential genetic modifier of CMT1A phenotypic expressions and offers a new pathway to therapeutic interventions. ANN NEUROL 2019;85:316-330.
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Affiliation(s)
- Feifei Tao
- Department for Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL
| | - Gary W Beecham
- Department for Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL
| | - Adriana P Rebelo
- Department for Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL
| | - John Svaren
- Department of Comparative Biosciences and Waisman Center, University of Wisconsin, Madison, WI
| | - Susan H Blanton
- Department for Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL
| | - John J Moran
- Department of Comparative Biosciences and Waisman Center, University of Wisconsin, Madison, WI
| | - Camila Lopez-Anido
- Department of Comparative Biosciences and Waisman Center, University of Wisconsin, Madison, WI
| | - Jasper M Morrow
- Medical Research Council Centre for Neuromuscular Diseases, University College London Institute of Neurology, London, United Kingdom
| | - Lisa Abreu
- Department for Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL
| | - Devon Rizzo
- Data Management and Coordinating Center, Rare Diseases Clinical Research Network, Pediatrics Epidemiology Center, University of South Florida, Tampa, FL
| | - Callyn A Kirk
- Data Management and Coordinating Center, Rare Diseases Clinical Research Network, Pediatrics Epidemiology Center, University of South Florida, Tampa, FL
| | - Xingyao Wu
- Department of Neurology, University of Iowa, Iowa City, IA
| | - Shawna Feely
- Department of Neurology, University of Iowa, Iowa City, IA
| | - Camiel Verhamme
- Department of Neurology, Academic Medical Center, Amsterdam, the Netherlands
| | | | | | - John W Day
- Department of Neurology, Stanford University, Palo Alto, CA
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jun Li
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI
| | - Sabrina W Yum
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Franco Taroni
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Frank Baas
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Davide Pareyson
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Steven S Scherer
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mary M Reilly
- Medical Research Council Centre for Neuromuscular Diseases, University College London Institute of Neurology, London, United Kingdom
| | - Michael E Shy
- Department of Neurology, University of Iowa, Iowa City, IA
| | - Stephan Züchner
- Department for Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL
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10
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Jiao X, Khan SY, Kaul H, Butt T, Naeem MA, Riazuddin S, Hejtmancik JF, Riazuddin SA. Autosomal recessive congenital cataracts linked to HSF4 in a consanguineous Pakistani family. PLoS One 2019; 14:e0225010. [PMID: 31815953 PMCID: PMC6901218 DOI: 10.1371/journal.pone.0225010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/25/2019] [Indexed: 11/17/2022] Open
Abstract
PURPOSE To investigate the genetic basis of autosomal recessive congenital cataracts (arCC) in a large consanguineous Pakistani family. METHODS All participating members of family, PKCC074 underwent an ophthalmic examination. Slit-lamp photographs were ascertained for affected individuals that have not been operated for the removal of the cataractous lens. A small aliquot of the blood sample was collected from all participating individuals and genomic DNAs were extracted. A genome-wide scan was performed with polymorphic short tandem repeat (STR) markers and the logarithm of odds (LOD) scores were calculated. All coding exons and exon-intron boundaries of HSF4 were sequenced and expression of Hsf4 in mouse ocular lens was investigated. The C-terminal FLAG-tagged wild-type and mutant HSF4b constructs were prepared to examine the nuclear localization pattern of the mutant protein. RESULTS The ophthalmological examinations suggested that nuclear cataracts are present in affected individuals. Genome-wide linkage analyses localized the critical interval to a 10.95 cM (14.17 Mb) interval on chromosome 16q with a maximum two-point LOD score of 4.51 at θ = 0. Sanger sequencing identified a novel missense mutation: c.433G>C (p.Ala145Pro) that segregated with the disease phenotype in the family and was not present in ethnically matched controls. Real-time PCR analysis identified the expression of HSF4 in mouse lens as early as embryonic day 15 with a steady level of expression thereafter. The immunofluorescence tracking confirmed that both wild-type and mutant HSF4 (p.Ala145Pro) proteins localized to the nucleus. CONCLUSION Here, we report a novel missense mutation in HSF4 associated with arCC in a familial case of Pakistani descent.
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Affiliation(s)
- Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Haiba Kaul
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tariq Butt
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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11
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Aryal S, Anand D, Hernandez FG, Weatherbee BAT, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. MS/MS in silico subtraction-based proteomic profiling as an approach to facilitate disease gene discovery: application to lens development and cataract. Hum Genet 2019; 139:151-184. [PMID: 31797049 DOI: 10.1007/s00439-019-02095-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/24/2019] [Indexed: 12/20/2022]
Abstract
While the bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery) effectively identifies human cataract-associated genes, it is currently based on just transcriptome data, and thus, it is necessary to include protein-level information to gain greater confidence in gene prioritization. Here, we expand iSyTE through development of a novel proteome-based resource on the lens and demonstrate its utility in cataract gene discovery. We applied high-throughput tandem mass spectrometry (MS/MS) to generate a global protein expression profile of mouse lens at embryonic day (E)14.5, which identified 2371 lens-expressed proteins. A major challenge of high-throughput expression profiling is identification of high-priority candidates among the thousands of expressed proteins. To address this problem, we generated new MS/MS proteome data on mouse whole embryonic body (WB). WB proteome was then used as a reference dataset for performing "in silico WB-subtraction" comparative analysis with the lens proteome, which effectively identified 422 proteins with lens-enriched expression at ≥ 2.5 average spectral counts, ≥ 2.0 fold enrichment (FDR < 0.01) cut-off. These top 20% candidates represent a rich pool of high-priority proteins in the lens including known human cataract-linked genes and many new potential regulators of lens development and homeostasis. This rich information is made publicly accessible through iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), which enables user-friendly visualization of promising candidates, thus making iSyTE a comprehensive tool for cataract gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Francisco G Hernandez
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Bailey A T Weatherbee
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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12
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Paradis H, Ahmad R, McDonald J, Boyce D, Gendron RL. Ocular tissue changes associated with anterior segment opacity in lumpfish (Cyclopterus lumpus L) eye. JOURNAL OF FISH DISEASES 2019; 42:1401-1408. [PMID: 31393016 DOI: 10.1111/jfd.13065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
Lumpfish use their vision to hunt prey or, in the case of aquaculture, to see and eat pelleted diets. A common anterior ocular opacity abnormality designated in the literature as "cataract" described in both farmed and wild lumpfish has not yet been characterized in detail at the pathobiological level. We describe here lens tissue changes associated with cataract in cultured and domesticated lumpfish. Methodology included gross observations, ophthalmoscopy and histology. Young adult cultured animals approaching 400 days post-hatch presented a range of anterior segment opacities associated with lenticular abnormalities observable at a histological level. Wild aged domesticated animals also displayed cataracts characterized mainly by abnormalities of the lens observed by both ophthalmoscopy and histology. Dysplastic lesions of the lens in one aged domesticated lumpfish were accompanied with both retinal and optic nerve degeneration. These novel naturally occurring anatomical changes in lumpfish present both commonalities and unique features associated with cataract in young adult cultured animals versus aged domesticated broodstock animals.
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Affiliation(s)
- Helene Paradis
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, NL, St. John's, Canada
| | - Raahyma Ahmad
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, NL, St. John's, Canada
| | - James McDonald
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, NL, St. John's, Canada
| | - Danny Boyce
- Department of Ocean Sciences, Memorial University, St. John's, NL, Canada
| | - Robert L Gendron
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, NL, St. John's, Canada
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13
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Kakrana A, Yang A, Anand D, Djordjevic D, Ramachandruni D, Singh A, Huang H, Ho JWK, Lachke SA. iSyTE 2.0: a database for expression-based gene discovery in the eye. Nucleic Acids Res 2019; 46:D875-D885. [PMID: 29036527 PMCID: PMC5753381 DOI: 10.1093/nar/gkx837] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/11/2017] [Indexed: 12/20/2022] Open
Abstract
Although successful in identifying new cataract-linked genes, the previous version of the database iSyTE (integrated Systems Tool for Eye gene discovery) was based on expression information on just three mouse lens stages and was functionally limited to visualization by only UCSC-Genome Browser tracks. To increase its efficacy, here we provide an enhanced iSyTE version 2.0 (URL: http://research.bioinformatics.udel.edu/iSyTE) based on well-curated, comprehensive genome-level lens expression data as a one-stop portal for the effective visualization and analysis of candidate genes in lens development and disease. iSyTE 2.0 includes all publicly available lens Affymetrix and Illumina microarray datasets representing a broad range of embryonic and postnatal stages from wild-type and specific gene-perturbation mouse mutants with eye defects. Further, we developed a new user-friendly web interface for direct access and cogent visualization of the curated expression data, which supports convenient searches and a range of downstream analyses. The utility of these new iSyTE 2.0 features is illustrated through examples of established genes associated with lens development and pathobiology, which serve as tutorials for its application by the end-user. iSyTE 2.0 will facilitate the prioritization of eye development and disease-linked candidate genes in studies involving transcriptomics or next-generation sequencing data, linkage analysis and GWAS approaches.
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Affiliation(s)
- Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Andrian Yang
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.,St. Vincent's Clinical School, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Djordje Djordjevic
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.,St. Vincent's Clinical School, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Deepti Ramachandruni
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Abhyudai Singh
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.,Department of Electrical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.,St. Vincent's Clinical School, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Salil A Lachke
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.,Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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14
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Wu SK, Priya R. Spatio-Temporal Regulation of RhoGTPases Signaling by Myosin II. Front Cell Dev Biol 2019; 7:90. [PMID: 31192208 PMCID: PMC6546806 DOI: 10.3389/fcell.2019.00090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/13/2019] [Indexed: 01/06/2023] Open
Abstract
RhoGTPase activation of non-muscle myosin II regulates cell division, extrusion, adhesion, migration, and tissue morphogenesis. However, the regulation of myosin II and mechanotransduction is not straightforward. Increasingly, the role of myosin II on the feedback regulation of RhoGTPase signaling is emerging. Indeed, myosin II controls RhoGTPase signaling through multiple mechanisms, namely contractility driven advection, scaffolding, and sequestration of signaling molecules. Here we discuss these mechanisms by which myosin II regulates RhoGTPase signaling in cell adhesion, migration, and tissue morphogenesis.
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Affiliation(s)
- Selwin K Wu
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Rashmi Priya
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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15
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Popp B, Agaimy A, Kraus C, Knaup KX, Ekici AB, Uebe S, Reis A, Wiesener M, Zweier C. Dissecting TSC2-mutated renal and hepatic angiomyolipomas in an individual with ARID1B-associated intellectual disability. BMC Cancer 2019; 19:435. [PMID: 31077186 PMCID: PMC6511147 DOI: 10.1186/s12885-019-5633-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 04/23/2019] [Indexed: 11/10/2022] Open
Abstract
Background Several subunits of the SWI/SNF chromatin remodeling complex are implicated in both cancer and neurodevelopmental disorders (NDD). Though there is no clinical evidence for an increased tumor risk in individuals with NDDs due to germline mutations in most of these genes so far, this has been repeatedly proposed and discussed. A young woman with NDD due to a de novo mutation in ARID1B now presented with a large renal (> 19 cm in diameter) and multiple hepatic angiomyolipomas (AMLs) but no other signs of tuberous sclerosis complex. Methods We analyzed tumor and healthy tissue samples with exome and panel sequencing. Results Additionally to the previously known, germline ARID1B variant we identified a post-zygotic truncating TSC2 variant in both renal and hepatic AMLs but not in any of the healthy tissues. We did not detect any further, obvious tumor driver events. The identification of a passenger variant in SIPA1L3 in both AMLs points to a common clonal origin. Metastasis of the renal AML into the liver is unlikely on the basis of discordant histopathological features. Our findings therefore point to very low-grade mosaicism for the TSC2 variant, possibly in a yet unknown mesenchymal precursor cell that expanded clonally during tumor development. A possible contribution of the germline ARID1B variant to the tumorigenesis remains unclear but cannot be excluded given the absence of any other evident tumor drivers in the AMLs. Conclusion This unique case highlights the blurred line between tumor genetics and post-zygotic events that can complicate exact molecular diagnoses in patients with rare manifestations. It also demonstrates the relevance of multiple disorders in a single individual, the challenges of detecting low-grade mosaicisms, and the importance of proper diagnosis for treatment and surveillance. Electronic supplementary material The online version of this article (10.1186/s12885-019-5633-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bernt Popp
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Karl X Knaup
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Michael Wiesener
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
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16
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Jiang J, Shihan MH, Wang Y, Duncan MK. Lens Epithelial Cells Initiate an Inflammatory Response Following Cataract Surgery. Invest Ophthalmol Vis Sci 2019; 59:4986-4997. [PMID: 30326070 PMCID: PMC6188467 DOI: 10.1167/iovs.18-25067] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Purpose Lens epithelial cell (LEC) conversion to myofibroblast is responsible for fibrotic cataract surgery complications including posterior capsular opacification. While transforming growth factor beta (TGFβ) signaling is important, the mechanisms by which the TGFβ pathway is activated post cataract surgery (PCS) are not well understood. Methods RNA-seq was performed on LECs obtained from a mouse cataract surgery model at the time of surgery and 24 hours later. Bioinformatic analysis was performed with iPathwayGuide. Expression dynamics were determined by immunofluorescence. Results The LEC transcriptome is massively altered by 24 hours PCS. The differentially expressed genes included those important for lens biology, and fibrotic markers. However, the most dramatic changes were in the expression of genes regulating the innate immune response, with the top three altered genes exhibiting greater than 1000-fold upregulation. Immunolocalization revealed that CXCL1, S100a9, CSF3, COX-2, CCL2, LCN2, and HMOX1 protein levels upregulate in LECs between 1 hour and 6 hours PCS and peak at 24 hours PCS, while their levels sharply attenuate by 3 days PCS. This massive upregulation of known inflammatory mediators precedes the infiltration of neutrophils into the eye at 18 hours PCS, the upregulation of canonical TGFβ signaling at 48 hours PCS, and the infiltration of macrophages at 3 days PCS. Conclusions These data demonstrate that LECs produce proinflammatory cytokines immediately following lens injury that could drive postsurgical flare, and suggest that inflammation may be a major player in the onset of lens-associated fibrotic disease PCS.
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Affiliation(s)
- Jian Jiang
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Biological Sciences, University of Delaware, Newark, Delaware, United States
| | - Mahbubul H Shihan
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States
| | - Yan Wang
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States
| | - Melinda K Duncan
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States
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17
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Anand D, Kakrana A, Siddam AD, Huang H, Saadi I, Lachke SA. RNA sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery. Hum Genet 2018; 137:941-954. [PMID: 30417254 DOI: 10.1007/s00439-018-1958-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/07/2018] [Indexed: 12/21/2022]
Abstract
Isolated or syndromic congenital cataracts are heterogeneous developmental defects, making the identification of the associated genes challenging. In the past, mouse lens expression microarrays have been successfully applied in bioinformatics tools (e.g., iSyTE) to facilitate human cataract-associated gene discovery. To develop a new resource for geneticists, we report high-throughput RNA sequencing (RNA-seq) profiles of mouse lens at key embryonic stages (E)10.5 (lens pit), E12.5 (primary fiber cell differentiation), E14.5 and E16.5 (secondary fiber cell differentiation). These stages capture important events as the lens develops from an invaginating placode into a transparent tissue. Previously, in silico whole-embryo body (WB)-subtraction-based "lens-enriched" expression has been effective in prioritizing cataract-linked genes. To apply an analogous approach, we generated new mouse WB RNA-seq datasets and show that in silico WB subtraction of lens RNA-seq datasets successfully identifies key genes based on lens-enriched expression. At ≥2 counts-per-million expression, ≥1.5 log2 fold-enrichment (p < 0.05) cutoff, E10.5 lens exhibits 1401 enriched genes (17% lens-expressed genes), E12.5 lens exhibits 1937 enriched genes (22% lens-expressed genes), E14.5 lens exhibits 2514 enriched genes (31% lens-expressed genes), and E16.5 lens exhibits 2745 enriched genes (34% lens-expressed genes). Biological pathway analysis identified genes associated with lens development, transcription regulation and signaling pathways, among other functional groups. Furthermore, these new RNA-seq data confirmed high expression of established cataract-linked genes and identified new potential regulators in the lens. Finally, we developed new lens stage-specific UCSC Genome Brower annotation tracks and made these publicly accessible through iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ) for user-friendly visualization of lens gene expression/enrichment to prioritize genes from high-throughput data from cataract cases.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, 19716, USA
| | - Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Irfan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, 19716, USA. .,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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18
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Reis LM, Semina EV. Genetic landscape of isolated pediatric cataracts: extreme heterogeneity and variable inheritance patterns within genes. Hum Genet 2018; 138:847-863. [PMID: 30187164 DOI: 10.1007/s00439-018-1932-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022]
Abstract
Pediatric cataract represents an important cause of pediatric visual impairment. While both genetic and environmental causes for pediatric cataract are known, a large proportion remains idiopathic. The purpose of this review is to discuss genes involved in isolated pediatric cataract, with a focus on variable inheritance patterns within genes. Mutations in over 52 genes are known to cause isolated pediatric cataract, with a major contribution from genes encoding for crystallins, transcription factors, membrane proteins, and cytoskeletal proteins. Interestingly, both dominant and recessive inheritance patterns have been reported for mutations in 13 different cataract genes. For some genes, dominant and recessive alleles represent distinct types of mutations, but for many, especially missense variants, there are no clear patterns to distinguish between dominant and recessive alleles. Further research into the functional effects of these mutations, as well as additional data on the frequency of the identified variants, is needed to clarify variant pathogenicity. Exome sequencing continues to be successful in identifying novel genes associated with congenital cataract but is hindered by the extreme genetic heterogeneity of this condition. The large number of idiopathic cases suggests that more genes and potentially novel mechanisms of gene disruption remain to be identified.
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Affiliation(s)
- Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA. .,Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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19
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de Vries M, van der Plaat DA, Vonk JM, Boezen HM. No association between DNA methylation and COPD in never and current smokers. BMJ Open Respir Res 2018; 5:e000282. [PMID: 30018765 PMCID: PMC6045732 DOI: 10.1136/bmjresp-2018-000282] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/07/2018] [Accepted: 06/09/2018] [Indexed: 12/04/2022] Open
Abstract
Introduction Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory lung disease with cigarette smoke as the main risk factor for its development. Since not every smoker develops COPD, other factors likely underlie differences in susceptibility to develop COPD. Here, we tested if DNA methylation may be such a factor by assessing the association between DNA methylation levels and COPD in never and current smokers from the general population. Methods For the current study, 1561 subjects were non-randomly selected from the LifeLines cohort study. We included 903 never smokers and 658 current smokers with and without COPD, defined as pre-bronchodilator forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) <70%. Subsequently, we performed robust regression analysis on whole blood DNA methylation levels of 420 938 CpG sites with COPD as outcome. Results None of the CpG sites in both the never and the current smokers were genome-wide significantly associated with COPD. CpG site cg14972228 annotated to SIPAL3 was most significant (p=5.66×10−6) in the never smokers, while CpG site cg08282037 annotated to EPS8L1 was most significant (p=1.45×10−5) in the current smokers. Conclusion In contrast to a previous, smaller study, we did not observe any significant association between DNA methylation levels and the presence of COPD, independent of smoking status. Apparently, DNA methylation studies are highly variable.
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Affiliation(s)
- Maaike de Vries
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Diana A van der Plaat
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
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20
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David D, Anand D, Araújo C, Gloss B, Fino J, Dinger M, Lindahl P, Pöyhönen M, Hannele L, Lavinha J. Identification of OAF and PVRL1 as candidate genes for an ocular anomaly characterized by Peters anomaly type 2 and ectopia lentis. Exp Eye Res 2018; 168:161-170. [PMID: 29305299 DOI: 10.1016/j.exer.2017.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 12/21/2017] [Accepted: 12/27/2017] [Indexed: 01/10/2023]
Abstract
Keratolenticular dysgenesis (KLD) and ectopia lentis are congenital eye defects. The aim of this study is the identification of molecular genetic alterations responsible for those ocular anomalies with neurologic impairment in an individual with a de novo balanced chromosome translocation t(11;18)(q23.3;q11.2)dn. Disruption of OAF, the human orthologue of the Drosophila oaf, by the 11q23.3 breakpoint results in reduced expression of this transcriptional regulator. Furthermore, four most likely nonfunctional chimeric transcripts comprising up to OAF exon 3, derived from the der(11) allele, have also been identified. This locus has been implicated by publicly available genome-wide association data in corneal disease and corneal topography. The expression of the poliovirus receptor-related 1(PVRL1) or nectin cell adhesion molecule 1 (NECTIN1), a paralogue of nectin cell adhesion molecule 3 (PVRL3) associated with congenital ocular defects, situated 500 kb upstream from 11q23.3 breakpoint, is increased. The 18q11.2 breakpoint is localized between cutaneous T-cell lymphoma-associated antigen 1(CTAGE1) and retinoblastoma binding protein 8 (RBBP8) genes. Genomic imbalance that could contribute to the observed phenotype was excluded. Analysis of gene expression datasets throughout normal murine ocular lens embryogenesis suggests that OAF expression is significantly enriched in the lens from early stages of development through adulthood, whereas PVRL1 is lens-enriched until E12.5 and then down-regulated. This contrasts with the observation that the proposita's lymphoblastoid cell lines exhibit low OAF and high PVRL1 expression as compared to control, which offers further support that the alterations described above are most likely responsible for the clinical phenotype. Finally, gene interaction topology data for PVRL1 also agree with our proposal that disruption of OAF by the translocation breakpoint and misregulation of PVRL1 due to a position effect contribute to the observed ocular and neurological phenotype.
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Affiliation(s)
- Dezső David
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal.
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Carlos Araújo
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal
| | - Brian Gloss
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Kensington, Australia
| | - Joana Fino
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal
| | - Marcel Dinger
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Kensington, Australia
| | - Päivi Lindahl
- Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Minna Pöyhönen
- Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Laivuori Hannele
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - João Lavinha
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal
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21
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A 16.7 kb deletion in Sipa1l3 is associated with juvenile cataract in mice. Mamm Genome 2017; 28:515-519. [PMID: 28951961 DOI: 10.1007/s00335-017-9720-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/21/2017] [Indexed: 10/18/2022]
Abstract
Congenital or juvenile cataract is a disease condition in which opacification of the lenses is present at birth or manifests early in life. It has been attributed to different monogenic factors with a high degree of heterogeneity and is often studied using mouse models. A spontaneous mutation was identified in a mouse line selected for heat loss that influenced lens formation and resulted in juvenile cataracts in mice homozygous for the recessive allele. Genetic dissection of this selection line by combining high-density genotypes and homozygosity mapping uncovered a 906 kb fragment on MMU7 encompassing 21 SNPs split into two groups of consecutive, homozygous segments specific to the cataract phenotype. Haplotype analysis revealed a 197.5 kb segment unique to cataract-affected mice that included a single known transcript consisting of the first 14 exons of Sipa1l3. In this region, we discovered a deletion of 1114 bp at the mRNA level, spanning four coding exons, predicted to produce a truncated Sipa1l3 protein lacking a portion of a Rap-GAP domain and two other potentially vital domains. At the genome level, the deletion consisted of 16,733 bp. Genotyping across different samples confirmed that only affected mice were homozygous for the deletion and normal mice were either heterozygous or homozygous for the wild-type allele. Further studies will be required to determine the impact of the truncated Sipa1l3 domains on eye development.
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22
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Cvekl A, Zhang X. Signaling and Gene Regulatory Networks in Mammalian Lens Development. Trends Genet 2017; 33:677-702. [PMID: 28867048 DOI: 10.1016/j.tig.2017.08.001] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 11/16/2022]
Abstract
Ocular lens development represents an advantageous system in which to study regulatory mechanisms governing cell fate decisions, extracellular signaling, cell and tissue organization, and the underlying gene regulatory networks. Spatiotemporally regulated domains of BMP, FGF, and other signaling molecules in late gastrula-early neurula stage embryos generate the border region between the neural plate and non-neural ectoderm from which multiple cell types, including lens progenitor cells, emerge and undergo initial tissue formation. Extracellular signaling and DNA-binding transcription factors govern lens and optic cup morphogenesis. Pax6, c-Maf, Hsf4, Prox1, Sox1, and a few additional factors regulate the expression of the lens structural proteins, the crystallins. Extensive crosstalk between a diverse array of signaling pathways controls the complexity and order of lens morphogenetic processes and lens transparency.
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Affiliation(s)
- Ales Cvekl
- Departments of Genetics and Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Xin Zhang
- Departments of Ophthalmology, Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.
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23
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Evers C, Staufner C, Granzow M, Paramasivam N, Hinderhofer K, Kaufmann L, Fischer C, Thiel C, Opladen T, Kotzaeridou U, Wiemann S, Schlesner M, Eils R, Kölker S, Bartram CR, Hoffmann GF, Moog U. Impact of clinical exomes in neurodevelopmental and neurometabolic disorders. Mol Genet Metab 2017; 121:297-307. [PMID: 28688840 DOI: 10.1016/j.ymgme.2017.06.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/29/2017] [Accepted: 06/29/2017] [Indexed: 01/06/2023]
Abstract
Whole exome sequencing (WES) is well established in research and is now being introduced into clinically indicated diagnostics (so-called clinical exomes). We evaluated the diagnostic yield and clinical implications of WES in 72 patients from 60 families with undiagnosed neurodevelopmental disorders (NDD), neurometabolic disorders, and dystonias. Pathogenic or likely pathogenic variants leading to a molecular diagnosis could be identified in 21 of the 60 families (overall 35%, in 36% of patients with NDD, in 43% of patients with neurometabolic disorders, in 25% of patients with dystonias). In one family two coexisting autosomal recessive diseases caused by homozygous pathogenic variants in two different genes were diagnosed. In another family, a homozygous frameshift variant in STRADA was found to cause a severe NDD with early onset epilepsy, brain anomalies, hypotonia, heart defect, nephrocalcinosis, macrocephaly and distinctive facies so far designated as PMSE (polyhydramnios, megalencephaly, symptomatic epilepsy) syndrome. In 7 of the 21 families with a molecular diagnosis the pathogenic variants were only identified by clinical follow-up, manual reevaluation of the literature, a change of filter setting, and/or reconsideration of inheritance pattern. Most importantly, clinical implications included management changes in 8 cases and impact on family planning in 20 families with a molecular diagnosis. This study shows that reevaluation and follow-up can improve the diagnostic rate and that WES results have important implications on medical management and family planning. Furthermore, we could confirm STRADA as a gene associated with syndromic ID but find it questionable if the current designation as PMSE depicts the most important clinical features.
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Affiliation(s)
- Christina Evers
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
| | - Christian Staufner
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Nagarajan Paramasivam
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Katrin Hinderhofer
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christine Fischer
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christian Thiel
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Thomas Opladen
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Urania Kotzaeridou
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Stefan Wiemann
- Genomics & Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefan Kölker
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Claus R Bartram
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Georg F Hoffmann
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Ute Moog
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
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24
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Shah B, Püschel AW. Regulation of Rap GTPases in mammalian neurons. Biol Chem 2017; 397:1055-69. [PMID: 27186679 DOI: 10.1515/hsz-2016-0165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/06/2016] [Indexed: 12/15/2022]
Abstract
Small GTPases are central regulators of many cellular processes. The highly conserved Rap GTPases perform essential functions in the mammalian nervous system during development and in mature neurons. During neocortical development, Rap1 is required to regulate cadherin- and integrin-mediated adhesion. In the adult nervous system Rap1 and Rap2 regulate the maturation and plasticity of dendritic spine and synapses. Although genetic studies have revealed important roles of Rap GTPases in neurons, their regulation by guanine nucleotide exchange factors (GEFs) that activate them and GTPase activating proteins (GAPs) that inactivate them by stimulating their intrinsic GTPase activity is just beginning to be explored in vivo. Here we review how GEFs and GAPs regulate Rap GTPases in the nervous system with a focus on their in vivo function.
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25
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Messina-Baas O, Cuevas-Covarrubias SA. Inherited Congenital Cataract: A Guide to Suspect the Genetic Etiology in the Cataract Genesis. Mol Syndromol 2017; 8:58-78. [PMID: 28611546 DOI: 10.1159/000455752] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2016] [Indexed: 01/23/2023] Open
Abstract
Cataracts are the principal cause of treatable blindness worldwide. Inherited congenital cataract (CC) shows all types of inheritance patterns in a syndromic and nonsyndromic form. There are more than 100 genes associated with cataract with a predominance of autosomal dominant inheritance. A cataract is defined as an opacity of the lens producing a variation of the refractive index of the lens. This variation derives from modifications in the lens structure resulting in light scattering, frequently a consequence of a significant concentration of high-molecular-weight protein aggregates. The aim of this review is to introduce a guide to identify the gene involved in inherited CC. Due to the manifold clinical and genetic heterogeneity, we discarded the cataract phenotype as a cardinal sign; a 4-group classification with the genes implicated in inherited CC is proposed. We consider that this classification will assist in identifying the probable gene involved in inherited CC.
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26
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Blanco-Sánchez B, Clément A, Phillips JB, Westerfield M. Zebrafish models of human eye and inner ear diseases. Methods Cell Biol 2016; 138:415-467. [PMID: 28129854 DOI: 10.1016/bs.mcb.2016.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Eye and inner ear diseases are the most common sensory impairments that greatly impact quality of life. Zebrafish have been intensively employed to understand the fundamental mechanisms underlying eye and inner ear development. The zebrafish visual and vestibulo-acoustic systems are very similar to these in humans, and although not yet mature, they are functional by 5days post-fertilization (dpf). In this chapter, we show how the zebrafish has significantly contributed to the field of biomedical research and how researchers, by establishing disease models and meticulously characterizing their phenotypes, have taken the first steps toward therapies. We review here models for (1) eye diseases, (2) ear diseases, and (3) syndromes affecting eye and/or ear. The use of new genome editing technologies and high-throughput screening systems should increase considerably the speed at which knowledge from zebrafish disease models is acquired, opening avenues for better diagnostics, treatments, and therapies.
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Affiliation(s)
| | - A Clément
- University of Oregon, Eugene, OR, United States
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27
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Rothe M, Monteiro F, Dietmann P, Kühl SJ. Comparative expression study of sipa family members during early Xenopus laevis development. Dev Genes Evol 2016; 226:369-82. [DOI: 10.1007/s00427-016-0556-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/28/2016] [Indexed: 01/20/2023]
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28
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Anand D, Lachke SA. Systems biology of lens development: A paradigm for disease gene discovery in the eye. Exp Eye Res 2016; 156:22-33. [PMID: 26992779 DOI: 10.1016/j.exer.2016.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/19/2022]
Abstract
Over the past several decades, the biology of the developing lens has been investigated using molecular genetics-based approaches in various vertebrate model systems. These efforts, involving target gene knockouts or knockdowns, have led to major advances in our understanding of lens morphogenesis and the pathological basis of cataracts, as well as of other lens related eye defects. In particular, we now have a functional understanding of regulators such as Pax6, Six3, Sox2, Oct1 (Pou2f1), Meis1, Pnox1, Zeb2 (Sip1), Mab21l1, Foxe3, Tfap2a (Ap2-alpha), Pitx3, Sox11, Prox1, Sox1, c-Maf, Mafg, Mafk, Hsf4, Fgfrs, Bmp7, and Tdrd7 in this tissue. However, whether these individual regulators interact or their targets overlap, and the significance of such interactions during lens morphogenesis, is not well defined. The arrival of high-throughput approaches for gene expression profiling (microarrays, RNA-sequencing (RNA-seq), etc.), which can be coupled with chromatin immunoprecipitation (ChIP) or RNA immunoprecipitation (RIP) assays, along with improved computational resources and publically available datasets (e.g. those containing comprehensive protein-protein, protein-DNA information), presents new opportunities to advance our understanding of the lens tissue on a global systems level. Such systems-level knowledge will lead to the derivation of the underlying lens gene regulatory network (GRN), defined as a circuit map of the regulator-target interactions functional in lens development, which can be applied to expedite cataract gene discovery. In this review, we cover the various systems-level approaches such as microarrays, RNA-seq, and ChIP that are already being applied to lens studies and discuss strategies for assembling and interpreting these vast amounts of high-throughput information for effective dispersion to the scientific community. In particular, we discuss strategies for effective interpretation of this new information in the context of the rich knowledge obtained through the application of traditional single-gene focused experiments on the lens. Finally, we discuss our vision for integrating these diverse high-throughput datasets in a single web-based user-friendly tool iSyTE (integrated Systems Tool for Eye gene discovery) - a resource that is already proving effective in the identification and characterization of genes linked to lens development and cataract. We anticipate that application of a similar approach to other ocular tissues such as the retina and the cornea, and even other organ systems, will significantly impact disease gene discovery.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
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29
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New mutations in DYNC2H1 and WDR60 genes revealed by whole-exome sequencing in two unrelated Sardinian families with Jeune asphyxiating thoracic dystrophy. Clin Chim Acta 2016; 455:172-80. [PMID: 26874042 DOI: 10.1016/j.cca.2016.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/11/2016] [Accepted: 02/09/2016] [Indexed: 12/30/2022]
Abstract
Jeune asphyxiating thoracic dystrophy (JATD; Jeune syndrome, MIM 208500) is a rare autosomal recessive chondrodysplasia, phenotypically overlapping with short-rib polydactyly syndromes (SRPS). JATD typical hallmarks include skeletal abnormalities such as narrow chest, shortened ribs, limbs shortened bones, extra fingers and toes (polydactyly), as well as extraskeletal manifestations (renal, liver and retinal disease). To date, disease-causing mutations have been found in several genes, highlighting a marked genetic heterogeneity that prevents a molecular diagnosis of the disease in most families. Here, we report the results of whole-exome sequencing (WES) carried out in four JATD cases, belonging to three unrelated families of Sardinian origin. The exome analysis allowed to identify mutations not previously reported in the DYNC2H1 (MIM 603297) and WDR60 (MIM 615462) genes, both codifying for ciliary intraflagellar transport components whose mutations are known to cause Jeune syndrome.
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30
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Rothe M, Kanwal N, Dietmann P, Seigfried F, Hempel A, Schütz D, Reim D, Engels R, Linnemann A, Schmeisser MJ, Bockmann J, Kühl M, Boeckers TM, Kühl SJ. An Epha4/Sipa1l3/Wnt pathway regulates eye development and lens maturation. Development 2016; 144:321-333. [DOI: 10.1242/dev.147462] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 01/21/2023]
Abstract
The signal-induced proliferation associated family of proteins comprises four members, SIPA1 and SIPA1L1-1L3. Mutations of the human SIPA1L3 gene result in congenital cataracts. In Xenopus, loss of Sipa1l3 function led to a severe eye phenotype that was distinguished by smaller eyes and lenses including lens fiber cell maturation defects. We found a direct interaction between Sipa1l3 and Epha4, building a functional platform for proper ocular development. Epha4 deficiency phenocopied loss of Sipa1l3 and rescue experiments demonstrated that Epha4 acts up-stream of Sipa1l3 during eye development. Both, Sipa1l3 and Epha4 are required for early eye specification. The ocular phenotype, upon loss of either Epha4 or Sipa1l3, was partially mediated by rax. We demonstrated that canonical Wnt signaling is inhibited downstream of Epha4/Sipa1l3 during normal eye development. Depletion of either Sipa1l3 or Epha4 resulted in an up-regulation of axin2 expression, a direct Wnt/β-catenin target gene. In line with this, Sipa1l3 or Epha4 depletion could be rescued by blocking Wnt/β-catenin or activating non-canonical Wnt signaling. We therefore conclude that this pathomechanism prevents proper eye development and maturation of lens fiber cells resulting in congenital cataracts.
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Affiliation(s)
- Melanie Rothe
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Noreen Kanwal
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Petra Dietmann
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Franziska Seigfried
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Annemarie Hempel
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Desiree Schütz
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Dominik Reim
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, 89081 Ulm University, Ulm, Germany
| | - Rebecca Engels
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Alexander Linnemann
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Michael J. Schmeisser
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
- Department of Neurology, Ulm University, 89081 Ulm, Germany
| | - Juergen Bockmann
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Tobias M. Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
| | - Susanne J. Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
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