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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. Hum Genet 2023; 142:927-947. [PMID: 37191732 PMCID: PMC10680127 DOI: 10.1007/s00439-023-02570-0] [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: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3300 proteins per sample (n = 5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ≥ 2.5 average spectral counts, ≥ 2.0 fold-enrichment, false discovery rate < 0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, 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, Newark, DE, 19716, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA.
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Leoni C, Viscogliosi G, Tartaglia M, Aoki Y, Zampino G. Multidisciplinary Management of Costello Syndrome: Current Perspectives. J Multidiscip Healthc 2022; 15:1277-1296. [PMID: 35677617 PMCID: PMC9169840 DOI: 10.2147/jmdh.s291757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Costello syndrome (CS) is a rare neurodevelopmental disorder caused by germline mutations in HRAS. It belongs among the RASopathies, a group of syndromes characterized by alterations in components of the RAS/MAPK signaling pathway and sharing overlapping phenotypes. Its typical features include a distinctive facial appearance, growth delay, intellectual disability, ectodermal, cardiac, and musculoskeletal abnormalities, and cancer predisposition. Due to the several comorbidities having a strong impact on the quality of life, a multidisciplinary team is essential in the management of such a condition from infancy to adult age, to promptly address any detected issue and to develop appropriate personalized follow-up protocols and treatment strategies. With the present paper we aim to highlight the core and ancillary medical disciplines involved in managing the health challenges characterizing CS from pediatric to adult age, according to literature and to our large clinical experience.
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Affiliation(s)
- Chiara Leoni
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Rome, Italy
- Correspondence: Chiara Leoni, Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Largo Gemelli 8, Rome, IT-00168, Italy, Tel +39-063381344, Fax +39-063383211, Email
| | - Germana Viscogliosi
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Giuseppe Zampino
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
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Shankar SP, Fallurin R, Watson T, Shankar PR, Young TL, Orel-Bixler D, Rauen KA. Ophthalmic manifestations in Costello syndrome caused by Ras pathway dysregulation during development. Ophthalmic Genet 2021; 43:48-57. [PMID: 34612139 DOI: 10.1080/13816810.2021.1978103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Costello syndrome (CS) is a multisystem developmental disorder caused by germline pathogenic variants in HRAS resulting in dysregulation of the Ras pathway. A systematic characterization of ophthalmic manifestations provides a unique opportunity to understand the role of Ras signal transduction in ocular development and guide optimal ophthalmic care in CS individuals. METHODS Visual function, ocular features and genotype/phenotype correlations were evaluated in CS individuals harboring HRAS pathogenic variants, by cross-sectional and retrospective studies, and were recruited through the Costello Syndrome Family Network (CSFN) between 2007 and 2020. RESULTS Fifty-six molecularly diagnosed CS individuals including 34 females and 22 males, ages ranging from 0.5 to 37 years were enrolled. The most common ophthalmic manifestations in the cross-sectional study were lack of stereopsis (96%), refractive errors (83%), strabismus (72%), nystagmus (69%), optic nerve hypoplasia or pallor (55%) and ptosis (13.7%) with higher prevalence than in the retrospective data (refractive errors (41%), strabismus (44%), nystagmus (26%), optic nerve hypoplasia or pallor (7%) and ptosis (11%)). Visual acuities were found to ranged from 20/25 to 20/800 and contrast sensitivity from 1.6% to 44%. HRAS pathogenic variants included p.G12S (84%), p.G13C (7%), p.G12A (5.4%), p.G12C (1.8%) and p.A146V (1.8%). CONCLUSION Majority of individuals with CS have refractive errors, strabismus, nystagmus, absent stereopsis, and optic nerve abnormalities suggesting that HRAS and the Ras pathway play a vital role in visual system development. Ptosis, refractive errors and strabismus are amenable to treatment and early ophthalmic evaluation is crucial to prevent long-term vision impairment and improve overall quality of life in CS.
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Affiliation(s)
- Suma P Shankar
- Department of Pediatrics, University of California Davis, Sacramento, California, USA.,Department of Ophthalmology, University of California Davis, Sacramento, California, USA
| | - Reshmitha Fallurin
- Department of Internal Medicine, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Tonya Watson
- The School of Optometry and Vision Science, University of California Berkeley, Berkeley, California, USA
| | - Prabhu R Shankar
- Department of Public Health, University of California Davis, Sacramento, California, USA
| | - Terri L Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Deborah Orel-Bixler
- The School of Optometry and Vision Science, University of California Berkeley, Berkeley, California, USA
| | - Katherine A Rauen
- Department of Pediatrics, University of California Davis, Sacramento, California, USA
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Choi N, Ko JM, Shin SH, Kim EK, Kim HS, Song MK, Choi CW. Phenotypic and Genetic Characteristics of Five Korean Patients with Costello Syndrome. Cytogenet Genome Res 2019; 158:184-191. [PMID: 31394527 DOI: 10.1159/000502045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2019] [Indexed: 12/27/2022] Open
Abstract
Costello syndrome (CS) is a rare genetic disorder characterized by distinctive facial appearance, cardiopulmonary complications, severe growth retardation, skin and skeletal defects, developmental delay, and tumor predisposition. CS is caused by heterozygous de novo mutations in the proto-oncogene HRAS, which is a component of the RAS/mitogen-activated protein kinase pathway. Herein, we reviewed the phenotypic and genetic features of 5 Korean patients who were genetically diagnosed with CS. Atrial tachycardia and polyhydramnios, which are important prenatal features for CS, were observed in 4 and 5 patients, respectively. The distinctive coarse facial appearances of the patients and presence of deep palmoplantar creases supported the clinical diagnosis of CS, which was confirmed by HRAS sequence analysis. Extremely poor postnatal growth was observed in all 5 patients. Further, all patients exhibited cardiac abnormalities; left ventricular hypertrophy and hypertrophic cardiomyopathy were observed in 3 patients. All 5 patients suffered from airway problems; 3 of them required intubation right after birth, and 2 of them received tracheostomy. One patient with a p.Gly12Ser mutation was diagnosed with retroperitoneal rhabdomyosarcoma alveolar type at the age of 5 years. Consistent with previous reports, both patients with p.Gly12Cys mutations died within the first year of life due to cardiopulmonary failure. Our study summarizes the characteristics of these 5 Korean patients with CS and, along with previous studies, provides clues for genotype-phenotype correlation in patients with CS.
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Gripp KW, Morse LA, Axelrad M, Chatfield KC, Chidekel A, Dobyns W, Doyle D, Kerr B, Lin AE, Schwartz DD, Sibbles BJ, Siegel D, Shankar SP, Stevenson DA, Thacker MM, Weaver KN, White SM, Rauen KA. Costello syndrome: Clinical phenotype, genotype, and management guidelines. Am J Med Genet A 2019; 179:1725-1744. [PMID: 31222966 DOI: 10.1002/ajmg.a.61270] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/22/2019] [Accepted: 06/01/2019] [Indexed: 12/16/2022]
Abstract
Costello syndrome (CS) is a RASopathy caused by activating germline mutations in HRAS. Due to ubiquitous HRAS gene expression, CS affects multiple organ systems and individuals are predisposed to cancer. Individuals with CS may have distinctive craniofacial features, cardiac anomalies, growth and developmental delays, as well as dermatological, orthopedic, ocular, and neurological issues; however, considerable overlap with other RASopathies exists. Medical evaluation requires an understanding of the multifaceted phenotype. Subspecialists may have limited experience in caring for these individuals because of the rarity of CS. Furthermore, the phenotypic presentation may vary with the underlying genotype. These guidelines were developed by an interdisciplinary team of experts in order to encourage timely health care practices and provide medical management guidelines for the primary and specialty care provider, as well as for the families and affected individuals across their lifespan. These guidelines are based on expert opinion and do not represent evidence-based guidelines due to the lack of data for this rare condition.
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Affiliation(s)
- Karen W Gripp
- Division of Medical Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware
| | | | - Marni Axelrad
- Psychology Section, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Kathryn C Chatfield
- Section of Cardiology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | - Aaron Chidekel
- Division of Pulmonology, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware
| | - William Dobyns
- Division of Medical Genetics, Seattle Children's Hospital, Seattle, Washington
| | - Daniel Doyle
- Division of Endocrinology, A.I. duPont Hospital for Children, Wilmington, Delaware
| | - Bronwyn Kerr
- Manchester Center for Genomic Medicine, University of Manchester, Manchester, UK
| | - Angela E Lin
- Medical Genetics Unit, Department of Pediatrics, MassGeneral Hospital for Children, Boston, Massachusetts
| | - David D Schwartz
- Psychology Section, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Barbara J Sibbles
- Division of Pediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Dawn Siegel
- Department of Dermatology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Suma P Shankar
- Division of Genomic Medicine, Department of Pediatrics, University of California Davis, Sacramento, California
| | - David A Stevenson
- Division of Medical Genetic, Department of Pediatrics, Stanford University, Palo Alto, California
| | - Mihir M Thacker
- Department of Orthopedic Surgery, Nemoirs-Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - K Nicole Weaver
- Division of Human Genetics, University of Cincinnati College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sue M White
- Victorian Clinical Genetics Services, Royal Children's Hospital, Victoria, Australia
| | - Katherine A Rauen
- Division of Genomic Medicine, Department of Pediatrics, University of California Davis, Sacramento, California
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