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Reis LM, Seese SE, Costakos D, Semina EV. Congenital anterior segment ocular disorders: Genotype-phenotype correlations and emerging novel mechanisms. Prog Retin Eye Res 2024; 102:101288. [PMID: 39097141 DOI: 10.1016/j.preteyeres.2024.101288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Development of the anterior segment of the eye requires reciprocal sequential interactions between the arising tissues, facilitated by numerous genetic factors. Disruption of any of these processes results in congenital anomalies in the affected tissue(s) leading to anterior segment disorders (ASD) including aniridia, Axenfeld-Rieger anomaly, congenital corneal opacities (Peters anomaly, cornea plana, congenital primary aphakia), and primary congenital glaucoma. Current understanding of the genetic factors involved in ASD remains incomplete, with approximately 50% overall receiving a genetic diagnosis. While some genes are strongly associated with a specific clinical diagnosis, the majority of known factors are linked with highly variable phenotypic presentations, with pathogenic variants in FOXC1, CYP1B1, and PITX2 associated with the broadest spectrum of ASD conditions. This review discusses typical clinical presentations including associated systemic features of various forms of ASD; the latest functional data and genotype-phenotype correlations related to 25 ASD factors including newly identified genes; promising novel candidates; and current and emerging treatments for these complex conditions. Recent developments of interest in the genetics of ASD include identification of phenotypic expansions for several factors, discovery of multiple modes of inheritance for some genes, and novel mechanisms including a growing number of non-coding variants and alleles affecting specific domains/residues and requiring further studies.
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Affiliation(s)
- Linda M Reis
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Sarah E Seese
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Deborah Costakos
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Elena V Semina
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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2
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Farris J, Khanna C, Smadbeck JB, Johnson SH, Bothun E, Kaplan T, Hoffman F, Polonis K, Oliver G, Reis LM, Semina EV, Rust L, Hoppman NL, Vasmatzis G, Marcou CA, Schimmenti LA, Klee EW. Complex balanced intrachromosomal rearrangement involving PITX2 identified as a cause of Axenfeld-Rieger Syndrome. Am J Med Genet A 2024; 194:e63542. [PMID: 38234180 PMCID: PMC11003841 DOI: 10.1002/ajmg.a.63542] [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: 08/28/2023] [Revised: 12/15/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
Axenfeld-Rieger Syndrome (ARS) type 1 is a rare autosomal dominant condition characterized by anterior chamber anomalies, umbilical defects, dental hypoplasia, and craniofacial anomalies, with Meckel's diverticulum in some individuals. Here, we describe a clinically ascertained female of childbearing age with ARS for whom clinical targeted sequencing and deletion/duplication analysis followed by clinical exome and genome sequencing resulted in no pathogenic variants or variants of unknown significance in PITX2 or FOXC1. Advanced bioinformatic analysis of the genome data identified a complex, balanced rearrangement disrupting PITX2. This case is the first reported intrachromosomal rearrangement leading to ARS, illustrating that for patients with compelling clinical phenotypes but negative genomic testing, additional bioinformatic analysis are essential to identify subtle genomic abnormalities in target genes.
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Affiliation(s)
- Joseph Farris
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Cheryl Khanna
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - James B Smadbeck
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Erick Bothun
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Tyler Kaplan
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Francis Hoffman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Katarzyna Polonis
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gavin Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Laura Rust
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
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Kumar A, Han Y, Oatts JT. Genetic changes and testing associated with childhood glaucoma: A systematic review. PLoS One 2024; 19:e0298883. [PMID: 38386645 PMCID: PMC10883561 DOI: 10.1371/journal.pone.0298883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Many forms of childhood glaucoma have been associated with underlying genetic changes, and variants in many genes have been described. Currently, testing is variable as there are no widely accepted guidelines for testing. This systematic review aimed to summarize the literature describing genetic changes and testing practices in childhood glaucoma. This systematic review was conducted in accordance with the Preferred Reporting Items for Systematic review and Meta-Analyses (PRISMA) 2020 guidelines and registered with Prospero (ID CRD42023400467). A comprehensive review of Pubmed, Embase, and Cochrane databases was performed from inception through March 2, 2023 using the search terms: (glaucoma) AND (pediatric OR childhood OR congenital OR child OR infant OR infantile) AND (gene OR genetic OR genotype OR locus OR genomic OR mutation OR variant OR test OR screen OR panel). Information was extracted regarding genetic variants including genotype-phenotype correlation. Risk of bias was assessed using the Newcastle-Ottawa Scale. Of 1,916 records screened, 196 studies met inclusion criteria and 53 genes were discussed. Among study populations, mean age±SD at glaucoma diagnosis was 8.94±9.54 years and 50.4% were male. The most common gene discussed was CYP1B1, evaluated in 109 (55.6%) studies. CYP1B1 variants were associated with region and population-specific prevalence ranging from 5% to 86% among those with primary congenital glaucoma. MYOC variants were discussed in 31 (15.8%) studies with prevalence up to 36% among patients with juvenile open angle glaucoma. FOXC1 variants were discussed in 25 (12.8%) studies, which demonstrated phenotypic severity dependent on degree of gene expression and type of mutation. Overall risk of bias was low; the most common domains of bias were selection and comparability. Numerous genes and genetic changes have been associated with childhood glaucoma. Understanding the most common genes as well as potential genotype-phenotype correlation has the potential to improve diagnostic and prognostic outcomes for children with glaucoma.
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Affiliation(s)
- Anika Kumar
- Department of Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Ying Han
- Department of Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Julius T. Oatts
- Department of Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
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Villalba MF, Li CM, Pakravan P, Bademci G, Chang TCP. Commercial Gene Panels for Congenital Anterior Segment Anomalies: Are They All the Same? Am J Ophthalmol 2023; 251:90-103. [PMID: 36906093 PMCID: PMC10247492 DOI: 10.1016/j.ajo.2023.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
PURPOSE We compared next generation sequencing multigene panels (NGS-MGP) from 5 commercial laboratories to inform ophthalmologists' decision making in diagnostic genetic testing for congenital anterior segment anomalies (CASAs). DESIGN Comparison of commercial genetic testing panels. METHODS This observational study gathered publicly available information on NGS-MGP from 5 commercial laboratories for the following: cataracts, glaucoma, anterior segment dysgenesis (ASD), microphthalmia-anophthalmia-coloboma (MAC), corneal dystrophies, and Axenfeld-Rieger syndrome (ARS). We compared gene panel composition, consensus rate (genes covered by all the panels per condition, "concurrent"), dissensus rate (genes covered by only 1 panel per condition, "standalone"), and intronic variant coverage. For individual genes, we compared publication history and association with systemic conditions. RESULTS Altogether, cataract, glaucoma, corneal dystrophies, MAC, ASD, and ARS panels tested 239, 60, 36, 292, and 10 discrete genes, respectively. The consensus rate varied between 16% and 50%, and the dissensus rate varied between 14% and 74%. After pooling concurrent genes from all conditions, 20% of these genes were concurrent in 2 or more conditions. For both cataract and glaucoma, concurrent genes had significantly stronger correlation with the condition than standalone genes. CONCLUSIONS The genetic testing of CASAs using NGS-MGPs is complicated, owing to their number, variety, and phenotypic and genetic overlap. Although the inclusion of additional genes, such as the standalone ones, might increase diagnostic yield, these genes are also less well studied, indicating uncertainty over their role in CASA pathogenesis. Rigorous prospective diagnostic yield studies of NGS-MGPs will aid in making decisions of panel selection for the diagnosis of CASAs.
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Affiliation(s)
- Maria Fernanda Villalba
- From the Bascom Palmer Eye Institute (M.F.V., T.C.P.C.), University of Miami Miller School of Medicine, Miami, Florida, USA; John P. Hussmann Institute for Human Genomics (M.F.V., G.B.), University of Miami Miller School of Medicine, Miami, Florida, USA; University of Miami Miller School of Medicine (M.F.V., C.M.L., P.P.), Miami, Florida, USA
| | - Chris Michael Li
- University of Miami Miller School of Medicine (M.F.V., C.M.L., P.P.), Miami, Florida, USA
| | - Parastou Pakravan
- University of Miami Miller School of Medicine (M.F.V., C.M.L., P.P.), Miami, Florida, USA
| | - Guney Bademci
- John P. Hussmann Institute for Human Genomics (M.F.V., G.B.), University of Miami Miller School of Medicine, Miami, Florida, USA; Department of Human Genetics (G.B.), University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Ta Chen Peter Chang
- From the Bascom Palmer Eye Institute (M.F.V., T.C.P.C.), University of Miami Miller School of Medicine, Miami, Florida, USA.
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Reis LM, Maheshwari M, Capasso J, Atilla H, Dudakova L, Thompson S, Zitano L, Lay-Son G, Lowry RB, Black J, Lee J, Shue A, Kremlikova Pourova R, Vaneckova M, Skalicka P, Jedlickova J, Trkova M, Williams B, Richard G, Bachman K, Seeley AH, Costakos D, Glaser TM, Levin AV, Liskova P, Murray JC, Semina EV. Axenfeld-Rieger syndrome: more than meets the eye. J Med Genet 2023; 60:368-379. [PMID: 35882526 PMCID: PMC9912354 DOI: 10.1136/jmg-2022-108646] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/15/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Axenfeld-Rieger syndrome (ARS) is characterised by typical anterior segment anomalies, with or without systemic features. The discovery of causative genes identified ARS subtypes with distinct phenotypes, but our understanding is incomplete, complicated by the rarity of the condition. METHODS Genetic and phenotypic characterisation of the largest reported ARS cohort through comprehensive genetic and clinical data analyses. RESULTS 128 individuals with causative variants in PITX2 or FOXC1, including 81 new cases, were investigated. Ocular anomalies showed significant overlap but with broader variability and earlier onset of glaucoma for FOXC1-related ARS. Systemic anomalies were seen in all individuals with PITX2-related ARS and the majority of those with FOXC1-related ARS. PITX2-related ARS demonstrated typical umbilical anomalies and dental microdontia/hypodontia/oligodontia, along with a novel high rate of Meckel diverticulum. FOXC1-related ARS exhibited characteristic hearing loss and congenital heart defects as well as previously unrecognised phenotypes of dental enamel hypoplasia and/or crowding, a range of skeletal and joint anomalies, hypotonia/early delay and feeding disorders with structural oesophageal anomalies in some. Brain imaging revealed highly penetrant white matter hyperintensities, colpocephaly/ventriculomegaly and frequent arachnoid cysts. The expanded phenotype of FOXC1-related ARS identified here was found to fully overlap features of De Hauwere syndrome. The results were used to generate gene-specific management plans for the two types of ARS. CONCLUSION Since clinical features of ARS vary significantly based on the affected gene, it is critical that families are provided with a gene-specific diagnosis, PITX2-related ARS or FOXC1-related ARS. De Hauwere syndrome is proposed to be a FOXC1opathy.
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Affiliation(s)
- Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
| | - Mohit Maheshwari
- Department of Pediatric Radiology, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
| | - Jenina Capasso
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Golisano Children's Hospital and University of Rochester, Rochester, New York, USA
| | - Huban Atilla
- Department of Ophthalmology, School of Medicine, Ankara University, Ankara, Turkey
| | - Lubica Dudakova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Samuel Thompson
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
| | - Lia Zitano
- Department of Medical Genetics, Spectrum Health, Grand Rapids, Michigan, USA
| | - Guillermo Lay-Son
- Unidad de Genética, División de Pediatría, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - R Brian Lowry
- Department of Clinical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Jennifer Black
- Center for Development, Behavior, and Genetics, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Joseph Lee
- Department of Family Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Ann Shue
- Byers Eye Institute, Department of Ophthalmology, Stanford University and Stanford Children's Health, Stanford, California, USA
| | - Radka Kremlikova Pourova
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Manuela Vaneckova
- Department of Radiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavlina Skalicka
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jana Jedlickova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marie Trkova
- Gennet, Centre for Fetal Medicine and Reproductive Genetics, Prague, Czech Republic
| | | | | | - Kristine Bachman
- Department of Pediatrics, Geisinger Medical Center, Danville, Pennsylvania, USA
| | - Andrea H Seeley
- Department of Pediatrics, Geisinger Medical Center, Danville, Pennsylvania, USA
| | - Deborah Costakos
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Thomas M Glaser
- Department of Cell Biology and Human Anatomy, UC-Davis School of Medicine, Davis, California, USA
| | - Alex V Levin
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Golisano Children's Hospital and University of Rochester, Rochester, New York, USA
| | - Petra Liskova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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6
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Villalba MF, Grajewski AL, Tekin M, Bademci G, Chang TC. Diagnostic yield of next generation sequencing gene panel assays for early-onset glaucoma in an ethnically diverse population. J AAPOS 2022; 26:302.e1-302.e6. [PMID: 36343799 PMCID: PMC9772253 DOI: 10.1016/j.jaapos.2022.08.529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/24/2022] [Accepted: 08/02/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Early-onset glaucoma is a potentially sight-threatening condition with high heritability. Next generation sequencing is a cost-effective alternative to individual gene screening that could expedite its diagnosis. However, the diagnostic yield of multigene panel assays for early-onset glaucoma varies according to the tested population. The purpose of this study was to ascertain the diagnostic yield of next generation sequencing panels in our cohort and to identify population characteristics that increase such yield. METHODS We conducted a retrospective review of the medical records of consecutive patients from November 2016 to August 2021 who were evaluated at our clinics for early-onset glaucoma and had undergone next generation sequencing panels for molecular diagnosis. RESULTS A total of 118 patients were included, in 22 of whom (19%) a causative variant was identified. Diagnostic yield varied by age of onset: of 60 patients with onset at <3 years of age, 19 (32%) had such variants identified. In contrast, of 58 patients with later-onset glaucoma, 3 (5%) had said variants identified (P = 0.0003). Other metrics that increased diagnostic yield were presence of additional ocular anomalies (P = 0.0092) and identifying ethnicity as White (compared with non-White, P = 0.0001). CONCLUSIONS In childhood glaucoma, earlier age of onset is correlated with higher likelihood of pathogenic variant identification. The large proportion of unsolved cases indicates a robust opportunity for gene discovery and genetic therapy targets in early-onset glaucoma patients.
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Affiliation(s)
- Maria Fernanda Villalba
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida; John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Alana L Grajewski
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Mustafa Tekin
- John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida; Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Guney Bademci
- John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Ta C Chang
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida.
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Ferre-Fernández JJ, Muheisen S, Thompson S, Semina EV. CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements. Hum Genomics 2022; 16:49. [PMID: 36284357 PMCID: PMC9597995 DOI: 10.1186/s40246-022-00423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
FOXC1 encodes a forkhead-domain transcription factor associated with several ocular disorders. Correct FOXC1 dosage is critical to normal development, yet the mechanisms controlling its expression remain unknown. Together with FOXQ1 and FOXF2, FOXC1 is part of a cluster of FOX genes conserved in vertebrates. CRISPR-Cas9-mediated dissection of genomic sequences surrounding two zebrafish orthologs of FOXC1 was performed. This included five zebrafish-human conserved regions, three downstream of foxc1a and two remotely upstream of foxf2a/foxc1a or foxf2b/foxc1b clusters, as well as two intergenic regions between foxc1a/b and foxf2a/b lacking sequence conservation but positionally corresponding to the area encompassing a previously reported glaucoma-associated SNP in humans. Removal of downstream sequences altered foxc1a expression; moreover, zebrafish carrying deletions of two or three downstream elements demonstrated abnormal phenotypes including enlargement of the anterior chamber of the eye reminiscent of human congenital glaucoma. Deletions of distant upstream conserved elements influenced the expression of foxf2a/b or foxq1a/b but not foxc1a/b within each cluster. Removal of either intergenic sequence reduced foxc1a or foxc1b expression during late development, suggesting a role in transcriptional regulation despite the lack of conservation at the nucleotide level. Further studies of the identified regions in human patients may explain additional individuals with developmental ocular disorders.
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Affiliation(s)
- Jesús-José Ferre-Fernández
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Sanaa Muheisen
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Samuel Thompson
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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Early-Onset Glaucoma in egl1 Mice Homozygous for Pitx2 Mutation. Biomedicines 2022; 10:biomedicines10030516. [PMID: 35327318 PMCID: PMC8945683 DOI: 10.3390/biomedicines10030516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/19/2022] [Indexed: 02/04/2023] Open
Abstract
Mutations in PITX2 cause Axenfeld–Rieger syndrome, with congenital glaucoma as an ocular feature. The egl1 mouse strain carries a chemically induced Pitx2 mutation and develops early-onset glaucoma. In this study, we characterized the glaucomatous features in egl1 mice. The eyes of egl1 and C57BL/6J control mice were assessed by slit lamp examination, total aqueous humor outflow facility, intraocular pressure (IOP) measurement, pattern electroretinography (PERG) recording, and histologic and immunohistochemistry assessment beginning at 3 weeks and up to 12 months of age. The egl1 mice developed elevated IOP as early as 4 weeks old. The IOP elevation was variable and asymmetric within and between the animals. The aqueous humor outflow facility was significantly reduced in 12-month-old animals. PERG detected a decreased response at 2 weeks after the development of IOP elevation. Retinal ganglion cell (RGC) loss was detected after 8 weeks of IOP elevation. Slit lamp and histologic evaluation revealed corneal opacity, iridocorneal adhesions (anterior synechiae), and ciliary body atrophy in egl1 mice. Immunohistochemistry assessment demonstrated glial cell activation and RGC axonal injury in response to IOP elevation. These results show that the eyes of egl1 mice exhibit anterior segment dysgenesis and early-onset glaucoma. The egl1 mouse strain may represent a useful model for the study of congenital glaucoma.
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9
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Hong Y, Luo Y. Zebrafish Model in Ophthalmology to Study Disease Mechanism and Drug Discovery. Pharmaceuticals (Basel) 2021; 14:ph14080716. [PMID: 34451814 PMCID: PMC8400593 DOI: 10.3390/ph14080716] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Visual impairment and blindness are common and seriously affect people’s work and quality of life in the world. Therefore, the effective therapies for eye diseases are of high priority. Zebrafish (Danio rerio) is an alternative vertebrate model as a useful tool for the mechanism elucidation and drug discovery of various eye disorders, such as cataracts, glaucoma, diabetic retinopathy, age-related macular degeneration, photoreceptor degeneration, etc. The genetic and embryonic accessibility of zebrafish in combination with a behavioral assessment of visual function has made it a very popular model in ophthalmology. Zebrafish has also been widely used in ocular drug discovery, such as the screening of new anti-angiogenic compounds or neuroprotective drugs, and the oculotoxicity test. In this review, we summarized the applications of zebrafish as the models of eye disorders to study disease mechanism and investigate novel drug treatments.
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Affiliation(s)
| | - Yan Luo
- Correspondence: ; Tel.: +86-020-87335931
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10
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Tran TQ, Kioussi C. Pitx genes in development and disease. Cell Mol Life Sci 2021; 78:4921-4938. [PMID: 33844046 PMCID: PMC11073205 DOI: 10.1007/s00018-021-03833-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/05/2021] [Accepted: 03/31/2021] [Indexed: 12/17/2022]
Abstract
Homeobox genes encode sequence-specific transcription factors (SSTFs) that recognize specific DNA sequences and regulate organogenesis in all eukaryotes. They are essential in specifying spatial and temporal cell identity and as a result, their mutations often cause severe developmental defects. Pitx genes belong to the PRD class of the highly evolutionary conserved homeobox genes in all animals. Vertebrates possess three Pitx paralogs, Pitx1, Pitx2, and Pitx3 while non-vertebrates have only one Pitx gene. The ancient role of regulating left-right (LR) asymmetry is conserved while new functions emerge to afford more complex body plan and functionalities. In mouse, Pitx1 regulates hindlimb tissue patterning and pituitary development. Pitx2 is essential for the development of the oral cavity and abdominal wall while regulates the formation and symmetry of other organs including pituitary, heart, gut, lung among others by controlling growth control genes upon activation of the Wnt/ß-catenin signaling pathway. Pitx3 is essential for lens development and migration and survival of the dopaminergic neurons of the substantia nigra. Pitx gene mutations are linked to various congenital defects and cancers in humans. Pitx gene family has the potential to offer a new approach in regenerative medicine and aid in identifying new drug targets.
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Affiliation(s)
- Thai Q Tran
- Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97331, USA
| | - Chrissa Kioussi
- Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97331, USA.
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11
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Sharma P, Sharma BS, Verma RJ. CRISPR-based genome editing of zebrafish. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:69-84. [PMID: 33934838 DOI: 10.1016/bs.pmbts.2021.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9, once discovered as an adaptive immune system in bacteria, has emerged as a disruptive technology in the field of genetic engineering. Technological advancements in the recent past has enhanced the applicability of CRISPR/Cas9 tool for gene editing, gene therapies, developmental studies and mutational analysis in various model organisms. Zebrafish, one of the excellent animal models, is preferred for conducting CRISPR/Cas9 studies to assess the functional implication of specific genes of interest. CRISPR/Cas9 mediated gene editing techniques, such as, knock-out and knock-in approaches, provide evidences to identify the role of different genes through loss-of-function studies. Also, CRISPR/Cas9 has been proved to be an efficient tool for designing disease models for gene expression studies based on phenotypic screening. The present chapter provides an overview of CRISPR/Cas9 mechanism, different strategies for DNA modifications and gene function analysis, highlighting the translational applications for future prospects, such as screening of drug toxicity and efficacy.
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Affiliation(s)
- Preeti Sharma
- Department of Zoology, Biomedical Technology & Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India; PanGenomics International Pvt Ltd, Sterling Accuris Diagnostics, Ellis Bridge, Ahmedabad, Gujarat, India.
| | - B Sharan Sharma
- Rivaara Labs Pvt Ltd, KD Hospital, Vaishnodevi Circle, Ahmedabad, Gujarat, India
| | - Ramtej J Verma
- Department of Zoology, Biomedical Technology & Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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Qin Y, Gao P, Yu S, Li J, Huang Y, Jia D, Tang Z, Li P, Liu F, Liu M. A large deletion spanning PITX2 and PANCR in a Chinese family with Axenfeld-Rieger syndrome. Mol Vis 2020; 26:670-678. [PMID: 33088171 PMCID: PMC7553719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 10/02/2020] [Indexed: 11/16/2022] Open
Abstract
Purpose To identify the genetic cause in a four-generation Chinese family with Axenfeld-Rieger syndrome (ARS). Methods The family members received clinical examinations of the eye, tooth, periumbilical skin, and heart. Sanger sequencing and whole-exome sequencing (WES) were performed to screen potential mutations. The genomic deletion region around the PITX2 gene was estimated from single nucleotide polymorphism (SNP) data from WES and then confirmed with "quantitative PCR (qPCR) using a set of primers. The DNA breakpoint was further identified with long-range PCR and Sanger sequencing. Results Symptoms including anterior segment dysplasia of the eye (iris dysplasia, multiple pupils, and posterior embryotoxon), dental dysplasia, and periumbilical skin redundancy were present in all of the affected individuals. Three of them had glaucoma. Corneal abnormalities (inferior sclerocornea, corneal endothelial dystrophy, and central corneal scar) were seen in most of the affected individuals. Cataract, limited eye movement, electrocardiographic abnormalities, intellectual disability, and recurrent miscarriages were observed in some of the affected individuals. No mutations in the coding and exon-intron adjacent regions of the PITX2 and FOXC1 genes were identified with Sanger sequencing. According to the SNP data from WES, we suspected that there might be a deletion region (at most 1.6 Mb) around the PITX2 gene. With the use of qPCR and long-range PCR, we identified a 53,840 bp deletion (chr4: 111,535,454-111,588,933) spanning PITX2 and PANCR. The genomic deletion cosegregated with the major ARS symptoms observed in the family members. Conclusions With the help of WES, qPCR, and long-range PCR, we identified a genomic deletion encompassing PITX2 and the adjacent noncoding gene PANCR in a Chinese family with ARS. The clinical features of the affected individuals are reported. This work may broaden understanding of the phenotypic and mutational spectrums related to ARS.
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Affiliation(s)
- Yayun Qin
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Pang Gao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jingzhen Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Pengcheng Li
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Fei Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
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Interpreting the impact of noncoding structural variation in neurodevelopmental disorders. Genet Med 2020; 23:34-46. [PMID: 32973355 PMCID: PMC7790743 DOI: 10.1038/s41436-020-00974-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
The emergence of novel sequencing technologies has greatly improved the identification of structural variation, revealing that a human genome harbors tens of thousands of structural variants (SVs). Since these SVs primarily impact noncoding DNA sequences, the next challenge is one of interpretation, not least to improve our understanding of human disease etiology. However, this task is severely complicated by the intricacy of the gene regulatory landscapes embedded within these noncoding regions, their incomplete annotation, as well as their dependence on the three-dimensional (3D) conformation of the genome. Also in the context of neurodevelopmental disorders (NDDs), reports of putatively causal, noncoding SVs are accumulating and understanding their impact on transcriptional regulation is presenting itself as the next step toward improved genetic diagnosis.
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Walter MA, Rezaie T, Hufnagel RB, Arno G. Ocular genetics in the genomics age. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:860-868. [PMID: 32896097 DOI: 10.1002/ajmg.c.31844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/29/2022]
Abstract
Current genetic screening methods for inherited eye diseases are concentrated on the coding exons of known disease genes (gene panels, clinical exome). These tests have a variable and often limited diagnostic rate depending on the clinical presentation, size of the gene panel and our understanding of the inheritance of the disorder (with examples described in this issue). There are numerous possible explanations for the missing heritability of these cases including undetected variants within the relevant gene (intronic, up/down-stream and structural variants), variants harbored in genes outside the targeted panel, intergenic variants, variants undetectable by the applied technology, complex/non-Mendelian inheritance, and nongenetic phenocopies. In this article we further explore and review methods to investigate these sources of missing heritability.
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Affiliation(s)
- Michael A Walter
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Tayebeh Rezaie
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gavin Arno
- University College London Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital, London, UK
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van der Lee R, Correard S, Wasserman WW. Deregulated Regulators: Disease-Causing cis Variants in Transcription Factor Genes. Trends Genet 2020; 36:523-539. [DOI: 10.1016/j.tig.2020.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
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16
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Lo Faro V, Siddiqui SN, Khan MI, Villanueva‐Mendoza C, Cortés‐González V, Jansonius N, Bergen AAB, Micheal S. Novel mutations in the PITX2 gene in Pakistani and Mexican families with Axenfeld-Rieger syndrome. Mol Genet Genomic Med 2020; 8:e1215. [PMID: 32400113 PMCID: PMC7336731 DOI: 10.1002/mgg3.1215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/12/2020] [Accepted: 02/24/2020] [Indexed: 01/13/2023] Open
Abstract
PURPOSE Axenfeld-Rieger syndrome (ARS) is a rare autosomal dominant disorder that affects the anterior segment of the eye. The aim of this study was to examine the PITX2 gene to identify possible novel mutations in Pakistani and Mexican families affected by the ARS phenotype. METHODS Three unrelated probands with a diagnosis of ARS were recruited for this study. Genomic DNA was isolated from the peripheral blood of the probands and their family members. Polymerase chain reaction and Sanger sequencing were used for the analysis of coding exons and the flanking intronic regions of the PITX2 gene. Bioinformatics tools and database (VarSome, Provean, and MutationTaster, SIFT, PolyPhen-2, and HOPE) were evaluated to explore missense variants. RESULTS We identified novel heterozygous variations in the PITX2 gene that segregated with the ARS phenotype within the families. The variant NM_153426.2(PITX2):c.226G > T or p.(Ala76Ser) and the mutation NM_153426.2(PITX2):c.455G > A or p.(Cys152Tyr) were identified in two Pakistani pedigrees, and the mutation NM_153426.2(PITX2):c.242_265del or p.(Lys81_Gln88del), segregated in a Mexican family. CONCLUSION Our study extends the spectrum of PITX2 mutations in individuals with ARS, enabling an improved diagnosis of this rare but serious syndrome.
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Affiliation(s)
- Valeria Lo Faro
- Department of Clinical GeneticsUniversity Medical Center (UMC)University of Amsterdam (UvA)AmsterdamThe Netherlands
- Department of OphthalmologyUniversity Medical Center Groningen (UMCG)University of Groningen (RUG)GroningenThe Netherlands
| | - Sorath N. Siddiqui
- Department of Pediatric Ophthalmology and StrabismusAl‐Shifa Eye Trust HospitalRawalpindiPakistan
| | - Muhammad I. Khan
- Department of Human GeneticsDonders Institute for BrainCognition and BehaviourRadboud UMCNijmegenThe Netherlands
| | | | | | - Nomdo Jansonius
- Department of OphthalmologyUniversity Medical Center Groningen (UMCG)University of Groningen (RUG)GroningenThe Netherlands
| | - Arthur A. B. Bergen
- Department of Clinical GeneticsUniversity Medical Center (UMC)University of Amsterdam (UvA)AmsterdamThe Netherlands
- Department of OphthalmologyUniversitair Medische Centre (UMC)University of Amsterdam (UvA)AmsterdamThe Netherlands
- The Netherlands Institute for Neurosciences (NIN‐KNAW)AmsterdamThe Netherlands
| | - Shazia Micheal
- Department of Clinical GeneticsUniversity Medical Center (UMC)University of Amsterdam (UvA)AmsterdamThe Netherlands
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Rubbini D, Cornet C, Terriente J, Di Donato V. CRISPR Meets Zebrafish: Accelerating the Discovery of New Therapeutic Targets. SLAS DISCOVERY 2020; 25:552-567. [PMID: 32462967 DOI: 10.1177/2472555220926920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bringing a new drug to the market costs an average of US$2.6 billion and takes more than 10 years from discovery to regulatory approval. Despite the need to reduce cost and time to increase productivity, pharma companies tend to crowd their efforts in the same indications and drug targets. This results in the commercialization of drugs that share the same mechanism of action (MoA) and, in many cases, equivalent efficacies among them-an outcome that helps neither patients nor the balance sheet of the companies trying to bring therapeutics to the same patient population. Indeed, the discovery of new therapeutic targets, based on a deeper understanding of the disease biology, would likely provide more innovative MoAs and potentially greater drug efficacies. It would also bring better chances for identifying appropriate treatments according to the patient's genetic stratification. Nowadays, we count with an enormous amount of unprocessed information on potential disease targets that could be extracted from omics data obtained from patient samples. In addition, hundreds of pharmacological and genetic screenings have been performed to identify innovative drug targets. Traditionally, rodents have been the animal models of choice to perform functional genomic studies. The high experimental cost, combined with the low throughput provided by those models, however, is a bottleneck for discovering and validating novel genetic disease associations. To overcome these limitations, we propose that zebrafish, in conjunction with the use of CRISPR/Cas9 genome-editing tools, could streamline functional genomic processes to bring biologically relevant knowledge on innovative disease targets in a shorter time frame.
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Affiliation(s)
- Davide Rubbini
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
| | - Carles Cornet
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
| | - Javier Terriente
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
| | - Vincenzo Di Donato
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
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Liu H, Barnes J, Pedrosa E, Herman NS, Salas F, Wang P, Zheng D, Lachman HM. Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations. J Neurodev Disord 2020; 12:14. [PMID: 32393163 PMCID: PMC7212686 DOI: 10.1186/s11689-020-09317-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Lowe syndrome (LS) is caused by loss-of-function mutations in the X-linked gene OCRL, which codes for an inositol polyphosphate 5-phosphatase that plays a key role in endosome recycling, clathrin-coated pit formation, and actin polymerization. It is characterized by congenital cataracts, intellectual and developmental disability, and renal proximal tubular dysfunction. Patients are also at high risk for developing glaucoma and seizures. We recently developed induced pluripotent stem cell (iPSC) lines from three patients with LS who have hypomorphic variants affecting the 3' end of the gene, and their neurotypical brothers to serve as controls. METHODS In this study, we used RNA sequencing (RNA-seq) to obtain transcriptome profiles in LS and control neural progenitor cells (NPCs). RESULTS In a comparison of the patient and control NPCs (n = 3), we found 16 differentially expressed genes (DEGs) at the multiple test adjusted p value (padj) < 0.1, with nine at padj < 0.05. Using nominal p value < 0.05, 319 DEGs were detected. The relatively small number of DEGs could be due to the fact that OCRL is not a transcription factor per se, although it could have secondary effects on gene expression through several different mechanisms. Although the number of DEGs passing multiple test correction was small, those that were found are quite consistent with some of the known molecular effects of OCRL protein, and the clinical manifestations of LS. Furthermore, using gene set enrichment analysis (GSEA), we found that genes increased expression in the patient NPCs showed enrichments of several gene ontology (GO) terms (false discovery rate < 0.25): telencephalon development, pallium development, NPC proliferation, and cortex development, which are consistent with a condition characterized by intellectual disabilities and psychiatric manifestations. In addition, a significant enrichment among the nominal DEGs for genes implicated in autism spectrum disorder (ASD) was found (e.g., AFF2, DNER, DPP6, DPP10, RELN, CACNA1C), as well as several that are strong candidate genes for the development of eye problems found in LS, including glaucoma. The most notable example is EFEMP1, a well-known candidate gene for glaucoma and other eye pathologies. CONCLUSION Overall, the RNA-seq findings present several candidate genes that could help explain the underlying basis for the neurodevelopmental and eye problems seen in boys with LS.
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Affiliation(s)
- Hequn Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jesse Barnes
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Nathaniel S. Herman
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Franklin Salas
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
- Dominick P Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Herbert M. Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, USA
- Dominick P Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
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Park DY, Cho SY, Jin DK, Kee C. Clinical Characteristics of Autosomal Dominant GJA1 Missense Mutation Linked to Oculodentodigital Dysplasia in a Korean Family. J Glaucoma 2020; 28:357-362. [PMID: 30628995 DOI: 10.1097/ijg.0000000000001190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE We aimed to present a comprehensive assessment of the ophthalmic characteristics of genetically confirmed oculodentodigital dysplasia (ODDD) in 4 members of a single Korean family across 3 generations. PATIENTS AND METHODS The characteristics of 4 affected ODDD patients were evaluated. Comprehensive ophthalmic and medical examinations were performed in 3 patients including the proband, together with genetic analysis, and retrospective chart review was conducted for an affected ancestor. For genetic analysis, targeted gene panel sequencing was conducted using genomic DNA extracted from peripheral blood. RESULTS All affected individuals in this family showed shared ophthalmic abnormalities of microcornea, microphthalmia, elevated intraocular pressure, and shallow anterior chamber, all of which have been reported as typical ocular features of ODDD. Myopic refractive error despite short axial length and thick cornea were highlighted as new findings of ODDD. Facial abnormalities were common in all affected members, but their fingers were normal. Severity of glaucoma was different among the affected individuals and seemed to depend on elevation of intraocular pressure, which occurred in narrow, but open-angle. Genetic analysis revealed the presence of c.119C>T (p.Ala40Val) in GJA1, which is responsible for ODDD, but not found in the control population. CONCLUSIONS This report describes detailed ocular characteristics in a genetically confirmed ODDD family, including unreported findings of thick cornea and myopic refractive error despite short axial length. The ocular features derived from the A40V mutation in GJA1 showed complete penetrance, suggesting a possible role of Cx43 in regulation of IOP and pathogenesis of glaucoma.
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Affiliation(s)
| | - Sung Yoon Cho
- Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Dong-Kyu Jin
- Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Lima Cunha D, Arno G, Corton M, Moosajee M. The Spectrum of PAX6 Mutations and Genotype-Phenotype Correlations in the Eye. Genes (Basel) 2019; 10:genes10121050. [PMID: 31861090 PMCID: PMC6947179 DOI: 10.3390/genes10121050] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 12/13/2022] Open
Abstract
The transcription factor PAX6 is essential in ocular development in vertebrates, being considered the master regulator of the eye. During eye development, it is essential for the correct patterning and formation of the multi-layered optic cup and it is involved in the developing lens and corneal epithelium. In adulthood, it is mostly expressed in cornea, iris, and lens. PAX6 is a dosage-sensitive gene and it is highly regulated by several elements located upstream, downstream, and within the gene. There are more than 500 different mutations described to affect PAX6 and its regulatory regions, the majority of which lead to PAX6 haploinsufficiency, causing several ocular and systemic abnormalities. Aniridia is an autosomal dominant disorder that is marked by the complete or partial absence of the iris, foveal hypoplasia, and nystagmus, and is caused by heterozygous PAX6 mutations. Other ocular abnormalities have also been associated with PAX6 changes, and genotype-phenotype correlations are emerging. This review will cover recent advancements in PAX6 regulation, particularly the role of several enhancers that are known to regulate PAX6 during eye development and disease. We will also present an updated overview of the mutation spectrum, where an increasing number of mutations in the non-coding regions have been reported. Novel genotype-phenotype correlations will also be discussed.
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Affiliation(s)
| | - Gavin Arno
- Institute of Ophthalmology, UCL, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital—Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Mariya Moosajee
- Institute of Ophthalmology, UCL, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- Correspondence:
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Perenthaler E, Yousefi S, Niggl E, Barakat TS. Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development. Front Cell Neurosci 2019; 13:352. [PMID: 31417368 PMCID: PMC6685065 DOI: 10.3389/fncel.2019.00352] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/16/2019] [Indexed: 12/22/2022] Open
Abstract
The development of the human cerebral cortex is a complex and dynamic process, in which neural stem cell proliferation, neuronal migration, and post-migratory neuronal organization need to occur in a well-organized fashion. Alterations at any of these crucial stages can result in malformations of cortical development (MCDs), a group of genetically heterogeneous neurodevelopmental disorders that present with developmental delay, intellectual disability and epilepsy. Recent progress in genetic technologies, such as next generation sequencing, most often focusing on all protein-coding exons (e.g., whole exome sequencing), allowed the discovery of more than a 100 genes associated with various types of MCDs. Although this has considerably increased the diagnostic yield, most MCD cases remain unexplained. As Whole Exome Sequencing investigates only a minor part of the human genome (1-2%), it is likely that patients, in which no disease-causing mutation has been identified, could harbor mutations in genomic regions beyond the exome. Even though functional annotation of non-coding regions is still lagging behind that of protein-coding genes, tremendous progress has been made in the field of gene regulation. One group of non-coding regulatory regions are enhancers, which can be distantly located upstream or downstream of genes and which can mediate temporal and tissue-specific transcriptional control via long-distance interactions with promoter regions. Although some examples exist in literature that link alterations of enhancers to genetic disorders, a widespread appreciation of the putative roles of these sequences in MCDs is still lacking. Here, we summarize the current state of knowledge on cis-regulatory regions and discuss novel technologies such as massively-parallel reporter assay systems, CRISPR-Cas9-based screens and computational approaches that help to further elucidate the emerging role of the non-coding genome in disease. Moreover, we discuss existing literature on mutations or copy number alterations of regulatory regions involved in brain development. We foresee that the future implementation of the knowledge obtained through ongoing gene regulation studies will benefit patients and will provide an explanation to part of the missing heritability of MCDs and other genetic disorders.
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Affiliation(s)
| | | | | | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC – University Medical Center, Rotterdam, Netherlands
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Hernández-Martínez N, González-Del Angel A, Alcántara-Ortigoza MA, González-Huerta LM, Cuevas-Covarrubias SA, Villanueva-Mendoza C. Molecular characterization of Axenfeld-Rieger spectrum and other anterior segment dysgeneses in a sample of Mexican patients. Ophthalmic Genet 2018; 39:728-734. [PMID: 30457409 DOI: 10.1080/13816810.2018.1547911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/24/2018] [Accepted: 10/21/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Anterior segment dysgenesis (ASD) and Axenfeld-Rieger spectrum (ARS) are mainly due to PITX2 and FOXC1 defects, but it is difficult in some patients to differentiate among PITX2-, FOXC1-, PAX6- and CYP1B1-related disorders. Here, we set out to characterize the pathogenic variants (PV) in PITX2, FOXC1, CYP1B1 and PAX6 in nine unrelated Mexican ARS/ASD patients and in their available affected/unaffected relatives. MATERIALS AND METHODS Automated Sanger sequencing of PITX2, FOXC1, PAX6 and CYP1B1 was performed; those patients without a PV were subsequently analyzed by Multiplex Ligation-dependent Probe Amplification (MLPA) for PITX2, FOXC1 and PAX6. Missense variants were evaluated with the MutPred, Provean, PMUT, SIFT, PolyPhen-2, CUPSAT and HOPE programs. RESULTS We identified three novel PV in PITX2 (NM_153427.2:c.217G>A, c.233T>C and c.279del) and two in FOXC1 [NM_001453.2:c.274C>T (novel) and c.454T>A] in five ARS patients. The previously reported FOXC1 c.367C>T or p.(Gln123*) variant was identified in a patient with ASD. The ocular phenotype related to FOXC1 included aniridia, corneal opacity and early onset glaucoma, while an asymmetric ocular phenotype and aniridia were associated with PITX2. No gene rearrangements were documented by MLPA analysis, nor were any PV identified in PAX6 or CYP1B1. CONCLUSIONS Heterozygous PV in the PITX2 and FOXC1 genes accounted for 66% (6/9) of the ARS/ASD cases. The absence of PAX6 or CYP1B1 abnormalities could reflect our small sample size, although their analysis could be justified in ARS/ASD patients that present with congenital glaucoma or aniridia.
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Affiliation(s)
| | | | | | - Luz M González-Huerta
- b Hospital General de México Dr. Eduardo Liceaga, Laboratorio de Investigación y Genética , México , México
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Cornet C, Di Donato V, Terriente J. Combining Zebrafish and CRISPR/Cas9: Toward a More Efficient Drug Discovery Pipeline. Front Pharmacol 2018; 9:703. [PMID: 30018554 PMCID: PMC6037853 DOI: 10.3389/fphar.2018.00703] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/11/2018] [Indexed: 12/13/2022] Open
Abstract
The use of zebrafish larvae in basic and applied research has grown exponentially during the last 20 years. The reasons for this success lay in its specific experimental advantages: on the one hand, the small size, the large number of progeny and the fast life cycle greatly facilitate large-scale approaches while maintaining 3Rs amenability; on the other hand, high genetic and physiological homology with humans and ease of genetic manipulation make zebrafish larvae a highly robust model for understanding human disease. Together, these advantages allow using zebrafish larvae for performing high-throughput research, both in terms of chemical and genetic phenotypic screenings. Therefore, the zebrafish larva as an animal model is placed between more reductionist in vitro high-throughput screenings and informative but low-throughput preclinical assays using mammals. However, despite its biological advantages and growing translational validation, zebrafish remains scarcely used in current drug discovery pipelines. In a context in which the pharmaceutical industry is facing a productivity crisis in bringing new drugs to the market, the combined advantages of zebrafish and the CRISPR/Cas9 system, the most powerful technology for genomic editing to date, has the potential to become a valuable tool for streamlining the generation of models mimicking human disease, the validation of novel drug targets and the discovery of new therapeutics. This review will focus on the most recent advances on CRISPR/Cas9 implementation in zebrafish and all their potential uses in biomedical research and drug discovery.
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Affiliation(s)
- Carles Cornet
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), Barcelona, Spain
| | - Vincenzo Di Donato
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), Barcelona, Spain
| | - Javier Terriente
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), Barcelona, Spain
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Hendee KE, Sorokina EA, Muheisen SS, Reis LM, Tyler RC, Markovic V, Cuturilo G, Link BA, Semina EV. PITX2 deficiency and associated human disease: insights from the zebrafish model. Hum Mol Genet 2018; 27:1675-1695. [PMID: 29506241 PMCID: PMC5932568 DOI: 10.1093/hmg/ddy074] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/30/2018] [Accepted: 02/26/2018] [Indexed: 02/06/2023] Open
Abstract
The PITX2 (paired-like homeodomain 2) gene encodes a bicoid-like homeodomain transcription factor linked with several human disorders. The main associated congenital phenotype is Axenfeld-Rieger syndrome, type 1, an autosomal dominant condition characterized by variable defects in the anterior segment of the eye, an increased risk of glaucoma, craniofacial dysmorphism and dental and umbilical anomalies; in addition to this, one report implicated PITX2 in ring dermoid of the cornea and a few others described cardiac phenotypes. We report three novel PITX2 mutations-c.271C > T, p.(Arg91Trp); c.259T > C, p.(Phe87Leu); and c.356delA, p.(Gln119Argfs*36)-identified in independent families with typical Axenfeld-Rieger syndrome characteristics and some unusual features such as corneal guttata, Wolf-Parkinson-White syndrome, and hyperextensibility. To gain further insight into the diverse roles of PITX2/pitx2 in vertebrate development, we generated various genetic lesions in the pitx2 gene via TALEN-mediated genome editing. Affected homozygous zebrafish demonstrated congenital defects consistent with the range of PITX2-associated human phenotypes: abnormal development of the cornea, iris and iridocorneal angle; corneal dermoids; and craniofacial dysmorphism. In addition, via comparison of pitx2M64* and wild-type embryonic ocular transcriptomes we defined molecular changes associated with pitx2 deficiency, thereby implicating processes potentially underlying disease pathology. This analysis identified numerous affected factors including several members of the Wnt pathway and collagen types I and V gene families. These data further support the link between PITX2 and the WNT pathway and suggest a new role in regulation of collagen gene expression during development.
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Affiliation(s)
- Kathryn E Hendee
- Department of Pediatrics and Children’s Research Institute Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Elena A Sorokina
- Department of Pediatrics and Children’s Research Institute Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Sanaa S Muheisen
- Department of Pediatrics and Children’s Research Institute Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Linda M Reis
- Department of Pediatrics and Children’s Research Institute Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebecca C Tyler
- Department of Pediatrics and Children’s Research Institute Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Vujica Markovic
- Faculty of Medicine, University of Belgrade, Serbia
- Clinical Centre of Serbia, University Eye Hospital, Belgrade, Serbia
| | - Goran Cuturilo
- Faculty of Medicine, University of Belgrade, Serbia
- Department of Medical Genetics, University Children’s Hospital, Belgrade, Serbia
| | - Brian A Link
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Elena V Semina
- Department of Pediatrics and Children’s Research Institute Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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