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Casey MJ, Chan PP, Li Q, Zu JF, Jette CA, Kohler M, Myers BR, Stewart RA. A simple and scalable zebrafish model of Sonic hedgehog medulloblastoma. Cell Rep 2024; 43:114559. [PMID: 39078737 PMCID: PMC11404834 DOI: 10.1016/j.celrep.2024.114559] [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: 01/05/2024] [Revised: 06/10/2024] [Accepted: 07/15/2024] [Indexed: 08/07/2024] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children and is stratified into three major subgroups. The Sonic hedgehog (SHH) subgroup represents ∼30% of all MB cases and has significant survival disparity depending upon TP53 status. Here, we describe a zebrafish model of SHH MB using CRISPR to create mutant ptch1, the primary genetic driver of human SHH MB. In these animals, tumors rapidly arise in the cerebellum and resemble human SHH MB by histology and comparative onco-genomics. Similar to human patients, MB tumors with loss of both ptch1 and tp53 have aggressive tumor histology and significantly worse survival outcomes. The simplicity and scalability of the ptch1-crispant MB model makes it highly amenable to CRISPR-based genome-editing screens to identify genes required for SHH MB tumor formation in vivo, and here we identify the gene encoding Grk3 kinase as one such target.
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Affiliation(s)
- Mattie J Casey
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Priya P Chan
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA; Primary Children's Hospital, Salt Lake City, UT 84113, USA
| | - Qing Li
- High-Throughput Genomics and Cancer Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Ju-Fen Zu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Cicely A Jette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Missia Kohler
- Department of Anatomic Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Benjamin R Myers
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Rodney A Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
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Bartek V, Szabó I, Harmath Á, Rudas G, Steiner T, Fintha A, Ács N, Beke A. Prenatal and Postnatal Diagnosis and Genetic Background of Corpus Callosum Malformations and Neonatal Follow-Up. CHILDREN (BASEL, SWITZERLAND) 2024; 11:797. [PMID: 39062246 PMCID: PMC11274835 DOI: 10.3390/children11070797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024]
Abstract
INTRODUCTION The corpus callosum is one of the five main cerebral commissures. It is key to combining sensory and motor functions. Its structure can be pathological (dysgenesis) or completely absent (agenesis). The corpus callosum dys- or agenesis is a rare disease (1:4000 live births), but it can have serious mental effects. METHODS In our study, we processed the data of 64 pregnant women. They attended a prenatal diagnostic center and genetic counseling from 2005 to 2019 at the Department of Obstetrics and Gynecology at Semmelweis University. RESULTS The pregnancies had the following outcomes: 52 ended in delivery, 1 in spontaneous abortion, and 11 in termination of pregnancy (TOP) cases (n = 64). The average time of detection with imaging tests was 25.24 gestational weeks. In 16 cases, prenatal magnetic resonance imaging (MRI) was performed. If the abnormality was detected before the 20th week, a genetic test was performed on an amniotic fluid sample obtained from a genetic amniocentesis. Karyotyping and cytogenetic tests were performed in 15 of the investigated cases. Karyotyping gave normal results in three cases (46,XX or XY). In one of these cases, postnatally chromosomal microarray (CMA) was later performed, which confirmed Aicardi syndrome (3q21.3-21.1 microdeletion). In one case, postnatally, the test found Wiedemann-Rautenstrauch syndrome. In other cases, it found X ring, Di George syndrome, 46,XY,del(13q)(q13q22) and 46,XX,del(5p)(p13) (Cri-du-chat syndrome). Edwards syndrome was diagnosed in six cases, and Patau syndrome in one case. CONCLUSIONS We found that corpus callosum abnormalities are often linked to chromosomal problems. We recommend that a cytogenetic test be performed in all cases to rule out inherited diseases. Also, the long-term outcome does not just depend on the disease's severity and the associated other conditions, and hence proper follow-up and early development are also key. For this reason, close teamwork between neonatology, developmental neurology, and pediatric surgery is vital.
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Affiliation(s)
- Virág Bartek
- Department of Obstetrics and Gynecology, Semmelweis University, 1085 Budapest, Hungary; (V.B.); (I.S.); (Á.H.); (T.S.); (N.Á.)
| | - István Szabó
- Department of Obstetrics and Gynecology, Semmelweis University, 1085 Budapest, Hungary; (V.B.); (I.S.); (Á.H.); (T.S.); (N.Á.)
| | - Ágnes Harmath
- Department of Obstetrics and Gynecology, Semmelweis University, 1085 Budapest, Hungary; (V.B.); (I.S.); (Á.H.); (T.S.); (N.Á.)
| | - Gábor Rudas
- Heim Pál National Pediatric Institute, 1089 Budapest, Hungary;
| | - Tidhar Steiner
- Department of Obstetrics and Gynecology, Semmelweis University, 1085 Budapest, Hungary; (V.B.); (I.S.); (Á.H.); (T.S.); (N.Á.)
| | - Attila Fintha
- Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary;
| | - Nándor Ács
- Department of Obstetrics and Gynecology, Semmelweis University, 1085 Budapest, Hungary; (V.B.); (I.S.); (Á.H.); (T.S.); (N.Á.)
| | - Artúr Beke
- Department of Obstetrics and Gynecology, Semmelweis University, 1085 Budapest, Hungary; (V.B.); (I.S.); (Á.H.); (T.S.); (N.Á.)
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Zambrano-Román M, Padilla-Gutiérrez JR, Valle Y, Muñoz-Valle JF, Guevara-Gutiérrez E, López-Olmos PA, Sepúlveda-Loza LC, Bautista-Herrera LA, Valdés-Alvarado E. PTCH1 Gene Variants, mRNA Expression, and Bioinformatics Insights in Mexican Cutaneous Squamous Cell Carcinoma Patients. BIOLOGY 2024; 13:191. [PMID: 38534460 DOI: 10.3390/biology13030191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Skin cancer is one of the most frequent types of cancer, and cutaneous squamous cell carcinoma (cSCC) constitutes 20% of non-melanoma skin cancer (NMSC) cases. PTCH1, a tumor suppressor gene involved in the Sonic hedgehog signaling pathway, plays a crucial role in neoplastic processes. METHODS An analytical cross-sectional study, encompassing 211 cSCC patients and 290 individuals in a control group (CG), was performed. A subgroup of samples was considered for the relative expression analysis, and the results were obtained using quantitative real-time PCR (qPCR) with TaqMan® probes. The functional, splicing, and disease-causing effects of the proposed variants were explored via bioinformatics. RESULTS cSCC was predominant in men, especially in sun-exposed areas such as the head and neck. No statistically significant differences were found regarding the rs357564, rs2236405, rs2297086, and rs41313327 variants of PTCH1, or in the risk of cSCC, nor in the mRNA expression between the cSCC group and CG. A functional effect of rs357564 and a disease-causing relation to rs41313327 was identified. CONCLUSION The proposed variants were not associated with cSCC risk in this Mexican population, but we recognize the need for analyzing larger population groups to elucidate the disease-causing role of rare variants.
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Affiliation(s)
- Marianela Zambrano-Román
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Jorge R Padilla-Gutiérrez
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Yeminia Valle
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - José Francisco Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Elizabeth Guevara-Gutiérrez
- Departamento de Dermatología, Instituto Dermatológico de Jalisco "Dr. José Barba Rubio", Secretaría de Salud Jalisco, Zapopan 45190, Mexico
| | - Patricia Aidé López-Olmos
- Departamento de Dermatología, Instituto Dermatológico de Jalisco "Dr. José Barba Rubio", Secretaría de Salud Jalisco, Zapopan 45190, Mexico
| | | | | | - Emmanuel Valdés-Alvarado
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
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Casey MJ, Chan PP, Li Q, Jette CA, Kohler M, Myers BR, Stewart RA. A Simple and Scalable Zebrafish Model of Sonic Hedgehog Medulloblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.03.577834. [PMID: 38370799 PMCID: PMC10871209 DOI: 10.1101/2024.02.03.577834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children and is stratified into three major subgroups. The Sonic hedgehog (SHH) subgroup represents ~30% of all MB cases and has significant survival disparity depending upon TP53 status. Here, we describe the first zebrafish model of SHH MB using CRISPR to mutate ptch1, the primary genetic driver in human SHH MB. These tumors rapidly arise adjacent to the valvula cerebelli and resemble human SHH MB by histology and comparative genomics. In addition, ptch1-deficient MB tumors with loss of tp53 have aggressive tumor histology and significantly worse survival outcomes, comparable to human patients. The simplicity and scalability of the ptch1 MB model makes it highly amenable to CRISPR-based genome editing screens to identify genes required for SHH MB tumor formation in vivo, and here we identify the grk3 kinase as one such target.
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Affiliation(s)
- Mattie J. Casey
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Priya P. Chan
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
- Primary Children’s Hospital, Salt Lake City, UT 84113, USA
| | - Qing Li
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Cicely A. Jette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Missia Kohler
- Department of Anatomic Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Benjamin R. Myers
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Rodney A. Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Lead contact
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Peng X, Chen M, Wang D, Han R, Gao T, Liu L, Liu C, Zhang K. Mutations of PTCH1 gene in two pedigrees with bifid rib-basal cell nevus-jaw cyst syndrome. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:223-229. [PMID: 37283107 PMCID: PMC10409912 DOI: 10.3724/zdxbyxb-2022-0492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/10/2022] [Indexed: 06/08/2023]
Abstract
Two male patients with bifid rib-basal cell nevus-jaw cyst syndrome (BCNS) were admitted to Department of Stomatology, the First Affiliated Hospital of Bengbu Medical College due to radiological findings of multiple low density shadows in the jaw. Clinical and imaging findings showed thoracic malformation, calcification of the tentorium cerebellum and falx cerebrum as well as widening of the orbital distance. Whole exon high-throughput sequencing was performed in two patients and their family members. The heterozygous mutations of c.C2541C>A(p.Y847X) and c.C1501C>T(p.Q501X) in PTCH1 gene were detected in both patients. Diagnosis of BCNS was confirmed. The heterozygous mutations of PTCH1 gene locus were also found in the mothers of the two probands. Proband 1 showed clinical manifestations of low intelligence, and heterozygous mutations of c.C2141T(p.P714L) and c.G3343A(p.V1115I) were detected in FANCD2 gene. Proband 2 had normal intelligence and no FANCD2 mutation. The fenestration decompression and curettage of jaw cyst were performed in both patients. Regular follow-up showed good bone growth at the original lesion, and no recurrence has been observed so far.
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Affiliation(s)
- Xiao Peng
- Department of Stomatology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui Province, China.
| | - Mo Chen
- Department of Stomatology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui Province, China
| | - Dong Wang
- Department of Stomatology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui Province, China
| | - Rui Han
- Department of Stomatology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui Province, China
| | - Tingyi Gao
- Department of Stomatology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui Province, China
| | - Liang Liu
- Department of Stomatology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui Province, China
| | - Chang Liu
- Department of Stomatology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui Province, China
| | - Kai Zhang
- Department of Stomatology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui Province, China.
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He Q, Hao X, Bao S, Wu X, Xu L, Hou Y, Huang Y, Peng L, Huang H, Ding Y, Zhao H. A392V and R945X mutations cause orofacial clefts via impairing PTCH1 function. Genomics 2022; 114:110507. [PMID: 36265746 DOI: 10.1016/j.ygeno.2022.110507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/30/2022] [Accepted: 10/16/2022] [Indexed: 01/15/2023]
Abstract
The Hedgehog (HH) signaling plays key roles in embryogenesis and organogenesis, and its dysfunction causes a variety of human birth defects. Orofacial cleft (OFC) is one of the most common congenital craniofacial defects, and its etiology is closely related to mutations in multiple components in the HH pathway, including the PTCH1 receptor. A quantity of PTCH1 variants have been associated with OFC, but the pathogenicity and underlying mechanism of these variants have not been functionally validated. In our previous studies, we identified two PTCH1 variants (A392V and R945X) in two families with hereditary OFC. Here we explore the functional consequences of these two variants. In zebrafish embryos, microinjection of wild type PTCH1 mRNA causes curved body axis and craniofacial anomalies. In contrast, microinjection of A392V and R945X PTCH1 mRNAs results in much milder phenotypes, suggesting these two variants are loss-of-function mutations. In mammalian cells, A392V and R945X mutations reverse the inhibitory effect of PTCH1 on HH signaling. Biochemically, the two mutants PTCH1 show lower expression levels and shortened half-life, indicting these mutations decrease the stability of PTCH1. A392V and R945X mutations also appear to cause PTCH1 to localize away from vesicles. Taken together, our findings indicate that A392V and R945X variants are loss-of-function mutations that disrupt the function of PTCH1 and thus cause dysregulation of HH signaling, leading to the pathogenesis of OFC.
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Affiliation(s)
- Qing He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Xingke Hao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Shanying Bao
- Department of Stomatology, Affiliated Hospital of Qinghai University, Xining, Qinghai, PR China
| | - Xiantao Wu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Linping Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Yuxia Hou
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China; Department of Orthodontics, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Yingjia Huang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Leiyuan Peng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Huimei Huang
- Department of Nephrology, Xi'an Children's Hospital, The Affiliated Children's Hospital of Xi'an Jiaotong University, PR China.
| | - Yi Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
| | - Huaxiang Zhao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China; Department of Orthodontics, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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Clinical variant interpretation and biologically relevant reference transcripts. NPJ Genom Med 2022; 7:59. [PMID: 36257961 PMCID: PMC9579139 DOI: 10.1038/s41525-022-00329-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/29/2022] [Indexed: 12/03/2022] Open
Abstract
Clinical variant interpretation is highly dependent on the choice of reference transcript. Although the longest transcript has traditionally been chosen as the reference, APPRIS principal and MANE Select transcripts, biologically supported reference sequences, are now available. In this study, we show that MANE Select and APPRIS principal transcripts are the best reference transcripts for clinical variation. APPRIS principal and MANE Select transcripts capture almost all ClinVar pathogenic variants, and they are particularly powerful over the 94% of coding genes in which they agree. We find that a vanishingly small number of ClinVar pathogenic variants affect alternative protein products. Alternative isoforms that are likely to be clinically relevant can be predicted using TRIFID scores, the highest scoring alternative transcripts are almost 700 times more likely to house pathogenic variants. We believe that APPRIS, MANE and TRIFID are essential tools for clinical variant interpretation.
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Ovejero D, Garcia-Giralt N, Martínez-Gil N, Rabionet R, Balcells S, Grinberg D, Pérez-Jurado LA, Nogués X, Etxebarria-Forondad I. Clinical description and genetic analysis of a novel familial skeletal dysplasia characterized by high bone mass and lucent bone lesions. Bone 2022; 161:116450. [PMID: 35623613 DOI: 10.1016/j.bone.2022.116450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/12/2022] [Accepted: 05/21/2022] [Indexed: 11/02/2022]
Abstract
High bone mass (HBM) disorders are a clinically and genetically heterogeneous subgroup of rare skeletal dysplasias. Here we present a case of a previously unreported familial skeletal dysplasia characterized by HBM and lucent bone lesions that we aimed to clinically characterize and genetically investigate. For phenotyping, we reviewed past clinical records and imaging tests, and performed physical examination (PE), bone densitometry, and mineral panels in affected individuals, including a male proband, his son and daughter, in addition to unaffected controls, including the proband's wife and brother. Affected individuals also underwent impact microindentation (IMI). In an effort to elucidate the disorder's molecular etiology, whole exome sequencing (WES) was performed in all individuals to filter for rare variants present only in affected ones. The cases displayed a unique skeletal phenotype with a mix of sclerotic features and lucent bone lesions, and high IMI values. Bone mineral density was very elevated in the proband and his daughter. The proband's daughter also exhibited idiopathic scoliosis (IS), in addition to mild thrombocytopenia and mild structural thyroid abnormalities, which were the only extra-skeletal abnormalities identified. WES analysis yielded 5 rare putative pathogenic variants in affected members in genes that are associated with bone metabolism including: SEM4AD, TBX18, PTCH1, PTK7, and ADGRE5. The PTK7 variant appeared as possibly implicated in the development of IS while the TBX18 and SEMA4D variants stood out as the strongest candidates for the lucent bone lesions and HBM, respectively, given their high predicted pathogenicity and putative role in bone biology. Variant functionality should be addressed in the future to assess their implication in skeletal metabolism as it is the first time that mutations in TBX18 and SEMA4D have been associated to bone developmental lesions and mineral metabolism in a clinical setting.
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Affiliation(s)
- Diana Ovejero
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain.
| | - Natalia Garcia-Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Núria Martínez-Gil
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Raquel Rabionet
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | | | - Xavier Nogués
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
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Yang Y, Wang X, Zhou D, Wei DQ, Peng S. SVPath: an accurate pipeline for predicting the pathogenicity of human exon structural variants. Brief Bioinform 2022; 23:6531897. [PMID: 35180781 DOI: 10.1093/bib/bbac014] [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: 09/24/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/12/2022] Open
Abstract
Although there are a large number of structural variations in the chromosomes of each individual, there is a lack of more accurate methods for identifying clinical pathogenic variants. Here, we proposed SVPath, a machine learning-based method to predict the pathogenicity of deletions, insertions and duplications structural variations that occur in exons. We constructed three types of annotation features for each structural variation event in the ClinVar database. First, we treated complex structural variations as multiple consecutive single nucleotide polymorphisms events, and annotated them with correlation scores based on single nucleic acid substitutions, such as the impact on protein function. Second, we determined which genes the variation occurred in, and constructed gene-based annotation features for each structural variation. Third, we also calculated related features based on the transcriptome, such as histone signal, the overlap ratio of variation and genomic element definitions, etc. Finally, we employed a gradient boosting decision tree machine learning method, and used the deletions, insertions and duplications in the ClinVar database to train a structural variation pathogenicity prediction model SVPath. These structural variations are clearly indicated as pathogenic or benign. Experimental results show that our SVPath has achieved excellent predictive performance and outperforms existing state-of-the-art tools. SVPath is very promising in evaluating the clinical pathogenicity of structural variants. SVPath can be used in clinical research to predict the clinical significance of unknown pathogenicity and new structural variation, so as to explore the relationship between diseases and structural variations in a computational way.
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Affiliation(s)
- Yaning Yang
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Xiaoqi Wang
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Deshan Zhou
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoliang Peng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.,School of Computer Science, National University of Defense Technology, Changsha, China.,Peng Cheng Lab, Shenzhen, China
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11
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Chesneau B, Aubert-Mucca M, Fremont F, Pechmeja J, Soler V, Isidor B, Nizon M, Dollfus H, Kaplan J, Fares-Taie L, Rozet JM, Busa T, Lacombe D, Naudion S, Amiel J, Rio M, Attie-Bitach T, Lesage C, Thouvenin D, Odent S, Morel G, Vincent-Delorme C, Boute O, Vanlerberghe C, Dieux A, Boussion S, Faivre L, Pinson L, Laffargue F, Le Guyader G, Le Meur G, Prieur F, Lambert V, Laudier B, Cottereau E, Ayuso C, Corton-Pérez M, Bouneau L, Le Caignec C, Gaston V, Jeanton-Scaramouche C, Dupin-Deguine D, Calvas P, Chassaing N, Plaisancié J. First evidence of SOX2 mutations in Peters' anomaly: lessons from molecular screening of 95 patients. Clin Genet 2022; 101:494-506. [PMID: 35170016 DOI: 10.1111/cge.14123] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 11/30/2022]
Abstract
Peters' anomaly (PA) is a rare anterior segment dysgenesis characterized by central corneal opacity and irido-lenticulo-corneal adhesions. Several genes are involved in syndromic or isolated PA (B3GLCT, PAX6, PITX3, FOXE3, CYP1B1). Some Copy Number Variations (CNVs) have also been occasionally reported. Despite this genetic heterogeneity, most of patients remain without genetic diagnosis. We retrieved a cohort of 95 individuals with PA and performed genotyping using a combination of Comparative genomic hybridization, whole genome, exome and targeted sequencing of 119 genes associated with ocular development anomalies. Causative genetic defects involving 12 genes and CNVs were identified for 1/3 of patients. Unsurprisingly, B3GLCT and PAX6 were the most frequently implicated genes, respectively in syndromic and isolated PA. Unexpectedly, the third gene involved in our cohort was SOX2, the major gene of micro-anophthalmia. Four unrelated patients with PA (isolated or with microphthalmia) were carrying pathogenic variants in this gene that was never associated with PA before. Here we described the largest cohort of PA patients ever reported. The genetic bases of PA are still to be explored as genetic diagnosis was unavailable for 2/3 of patients. Nevertheless, we showed here for the first time the involvement of SOX2 in PA, offering new evidence for its role in corneal transparency and anterior segment development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bertrand Chesneau
- Génétique Médicale, Hôpital Purpan, CHU, Toulouse, France.,Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU, Toulouse, France
| | | | - Félix Fremont
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU, Toulouse, France.,Service d'ophtalmologie, Hôpital Purpan, CHU Toulouse, France
| | - Jacmine Pechmeja
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU, Toulouse, France.,Service d'ophtalmologie, Hôpital Purpan, CHU Toulouse, France
| | - Vincent Soler
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU, Toulouse, France.,Service d'ophtalmologie, Hôpital Purpan, CHU Toulouse, France
| | - Bertrand Isidor
- Génétique Médicale, Institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Mathilde Nizon
- Génétique Médicale, Institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Hélène Dollfus
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpitaux Universitaires, Strasbourg, France
| | - Josseline Kaplan
- Laboratoire de Génétique Ophtalmologique, INSERM U1163, Institut Imagine, Paris, France
| | - Lucas Fares-Taie
- Laboratoire de Génétique Ophtalmologique, INSERM U1163, Institut Imagine, Paris, France
| | - Jean-Michel Rozet
- Laboratoire de Génétique Ophtalmologique, INSERM U1163, Institut Imagine, Paris, France
| | - Tiffany Busa
- Génétique Clinique, AP- HM CHU Timone Enfants, Marseille, France
| | - Didier Lacombe
- Département de Génétique Médicale, CHU Bordeaux, Bordeaux, France
| | - Sophie Naudion
- Département de Génétique Médicale, CHU Bordeaux, Bordeaux, France
| | - Jeanne Amiel
- Service de Génétique Médicale, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Marlène Rio
- Service de Génétique Médicale, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Tania Attie-Bitach
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-, HP, Paris, France
| | | | | | - Sylvie Odent
- Service de Génétique Clinique, Centre Labellisé pour les Anomalies du Développement Ouest, CHU Rennes; Institut de Génétique et Développement de Rennes, CNRS, UMR 6290, Université de Rennes, ERN ITHACA, France
| | - Godelieve Morel
- Service de Génétique Clinique, Centre Labellisé pour les Anomalies du Développement Ouest, CHU Rennes; Institut de Génétique et Développement de Rennes, CNRS, UMR 6290, Université de Rennes, ERN ITHACA, France
| | | | | | | | | | | | - Laurence Faivre
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU, Dijon, France
| | - Lucile Pinson
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, France
| | | | | | | | | | - Victor Lambert
- Service d'ophtalmologie, Hôpital Nord, Saint-Etienne, France
| | | | | | - Carmen Ayuso
- Genetics & Genomics Department, Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD-UAM). Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Marta Corton-Pérez
- Genetics & Genomics Department, Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD-UAM). Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | | | | | | | | | | | - Patrick Calvas
- Génétique Médicale, Hôpital Purpan, CHU, Toulouse, France.,Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU, Toulouse, France
| | - Nicolas Chassaing
- Génétique Médicale, Hôpital Purpan, CHU, Toulouse, France.,Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU, Toulouse, France
| | - Julie Plaisancié
- Génétique Médicale, Hôpital Purpan, CHU, Toulouse, France.,Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU, Toulouse, France.,INSERM U1214, ToNIC, Université Toulouse III, France
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12
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Kundishora AJ, Singh AK, Allington G, Duy PQ, Ryou J, Alper SL, Jin SC, Kahle KT. Genomics of human congenital hydrocephalus. Childs Nerv Syst 2021; 37:3325-3340. [PMID: 34232380 DOI: 10.1007/s00381-021-05230-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022]
Abstract
Congenital hydrocephalus (CH), characterized by enlarged brain ventricles, is considered a disease of pathological cerebrospinal fluid (CSF) accumulation and, therefore, treated largely by neurosurgical CSF diversion. The persistence of ventriculomegaly and poor neurodevelopmental outcomes in some post-surgical patients highlights our limited knowledge of disease mechanisms. Recent whole-exome sequencing (WES) studies have shown that rare, damaging de novo and inherited mutations with large effect contribute to ~ 25% of sporadic CH. Interestingly, multiple CH genes are key regulators of neural stem cell growth and differentiation and converge in human transcriptional networks and cell types pertinent to fetal neurogliogenesis. These data implicate genetic disruption of early brain development as the primary pathomechanism in a substantial minority of patients with sporadic CH, shedding new light on human brain development and the pathogenesis of hydrocephalus. These data further suggest WES as a clinical tool with potential to re-classify CH according to a molecular nomenclature of increased precision and utility for genetic counseling, outcome prognostication, and treatment stratification.
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Affiliation(s)
- Adam J Kundishora
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Amrita K Singh
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Garrett Allington
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Jian Ryou
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.
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13
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Susak H, Serra-Saurina L, Demidov G, Rabionet R, Domènech L, Bosio M, Muyas F, Estivill X, Escaramís G, Ossowski S. Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation. PLoS Comput Biol 2021; 17:e1007784. [PMID: 33606672 PMCID: PMC7928502 DOI: 10.1371/journal.pcbi.1007784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/03/2021] [Accepted: 01/04/2021] [Indexed: 12/02/2022] Open
Abstract
Rare variants are thought to play an important role in the etiology of complex diseases and may explain a significant fraction of the missing heritability in genetic disease studies. Next-generation sequencing facilitates the association of rare variants in coding or regulatory regions with complex diseases in large cohorts at genome-wide scale. However, rare variant association studies (RVAS) still lack power when cohorts are small to medium-sized and if genetic variation explains a small fraction of phenotypic variance. Here we present a novel Bayesian rare variant Association Test using Integrated Nested Laplace Approximation (BATI). Unlike existing RVAS tests, BATI allows integration of individual or variant-specific features as covariates, while efficiently performing inference based on full model estimation. We demonstrate that BATI outperforms established RVAS methods on realistic, semi-synthetic whole-exome sequencing cohorts, especially when using meaningful biological context, such as functional annotation. We show that BATI achieves power above 70% in scenarios in which competing tests fail to identify risk genes, e.g. when risk variants in sum explain less than 0.5% of phenotypic variance. We have integrated BATI, together with five existing RVAS tests in the 'Rare Variant Genome Wide Association Study' (rvGWAS) framework for data analyzed by whole-exome or whole genome sequencing. rvGWAS supports rare variant association for genes or any other biological unit such as promoters, while allowing the analysis of essential functionalities like quality control or filtering. Applying rvGWAS to a Chronic Lymphocytic Leukemia study we identified eight candidate predisposition genes, including EHMT2 and COPS7A.
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Affiliation(s)
- Hana Susak
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Laura Serra-Saurina
- Biomedical Research Networking Centre consortium of Public Health and Epidemiology (CIBERESP), Madrid, Spain
- Center for research in occupational Health (CiSAL), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Research Group on Statistics, Econometrics and Health (GRECS), Universitat de Girona (UdG), Girona, Spain
| | - German Demidov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Raquel Rabionet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, IBUB, Universitat de Barcelona; CIBERER, IRSJD, Barcelona, Spain
| | - Laura Domènech
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Biomedical Research Networking Centre consortium of Public Health and Epidemiology (CIBERESP), Madrid, Spain
| | - Mattia Bosio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francesc Muyas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Women’s Health Dexeus, Barcelona, Spain
| | - Geòrgia Escaramís
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Biomedical Research Networking Centre consortium of Public Health and Epidemiology (CIBERESP), Madrid, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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14
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Haug P, Koller S, Maggi J, Lang E, Feil S, Wlodarczyk A, Bähr L, Steindl K, Rohrbach M, Gerth-Kahlert C, Berger W. Whole Exome Sequencing in Coloboma/Microphthalmia: Identification of Novel and Recurrent Variants in Seven Genes. Genes (Basel) 2021; 12:65. [PMID: 33418956 PMCID: PMC7825129 DOI: 10.3390/genes12010065] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/25/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022] Open
Abstract
Coloboma and microphthalmia (C/M) are related congenital eye malformations, which can cause significant visual impairment. Molecular diagnosis is challenging as the genes associated to date with C/M account for only a small percentage of cases. Overall, the genetic cause remains unknown in up to 80% of patients. High throughput DNA sequencing technologies, including whole-exome sequencing (WES), are therefore a useful and efficient tool for genetic screening and identification of new mutations and novel genes in C/M. In this study, we analyzed the DNA of 19 patients with C/M from 15 unrelated families using singleton WES and data analysis for 307 genes of interest. We identified seven novel and one recurrent potentially disease-causing variants in CRIM1, CHD7, FAT1, PTCH1, PUF60, BRPF1, and TGFB2 in 47% of our families, three of which occurred de novo. The detection rate in patients with ocular and extraocular manifestations (67%) was higher than in patients with an isolated ocular phenotype (46%). Our study highlights the significant genetic heterogeneity in C/M cohorts and emphasizes the diagnostic power of WES for the screening of patients and families with C/M.
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Affiliation(s)
- Patricia Haug
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Elena Lang
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
- Department of Ophthalmology, University Hospital and University of Zurich, 8091 Zurich, Switzerland;
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Agnès Wlodarczyk
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Luzy Bähr
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland;
| | - Marianne Rohrbach
- Division of Metabolism and Children’s Research Centre, University Children’s Hospital Zurich, 8032 Zurich, Switzerland;
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital and University of Zurich, 8091 Zurich, Switzerland;
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8006 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8006 Zurich, Switzerland
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15
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Harding P, Cunha DL, Moosajee M. Animal and cellular models of microphthalmia. THERAPEUTIC ADVANCES IN RARE DISEASE 2021; 2:2633004021997447. [PMID: 37181112 PMCID: PMC10032472 DOI: 10.1177/2633004021997447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/02/2021] [Indexed: 05/16/2023]
Abstract
Microphthalmia is a rare developmental eye disorder affecting 1 in 7000 births. It is defined as a small (axial length ⩾2 standard deviations below the age-adjusted mean) underdeveloped eye, caused by disruption of ocular development through genetic or environmental factors in the first trimester of pregnancy. Clinical phenotypic heterogeneity exists amongst patients with varying levels of severity, and associated ocular and systemic features. Up to 11% of blind children are reported to have microphthalmia, yet currently no treatments are available. By identifying the aetiology of microphthalmia and understanding how the mechanisms of eye development are disrupted, we can gain a better understanding of the pathogenesis. Animal models, mainly mouse, zebrafish and Xenopus, have provided extensive information on the genetic regulation of oculogenesis, and how perturbation of these pathways leads to microphthalmia. However, differences exist between species, hence cellular models, such as patient-derived induced pluripotent stem cell (iPSC) optic vesicles, are now being used to provide greater insights into the human disease process. Progress in 3D cellular modelling techniques has enhanced the ability of researchers to study interactions of different cell types during eye development. Through improved molecular knowledge of microphthalmia, preventative or postnatal therapies may be developed, together with establishing genotype-phenotype correlations in order to provide patients with the appropriate prognosis, multidisciplinary care and informed genetic counselling. This review summarises some key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future. Plain language summary Animal and Cellular Models of the Eye Disorder, Microphthalmia (Small Eye) Microphthalmia, meaning a small, underdeveloped eye, is a rare disorder that children are born with. Genetic changes or variations in the environment during the first 3 months of pregnancy can disrupt early development of the eye, resulting in microphthalmia. Up to 11% of blind children have microphthalmia, yet currently no treatments are available. By understanding the genes necessary for eye development, we can determine how disruption by genetic changes or environmental factors can cause this condition. This helps us understand why microphthalmia occurs, and ensure patients are provided with the appropriate clinical care and genetic counselling advice. Additionally, by understanding the causes of microphthalmia, researchers can develop treatments to prevent or reduce the severity of this condition. Animal models, particularly mice, zebrafish and frogs, which can also develop small eyes due to the same genetic/environmental changes, have helped us understand the genes which are important for eye development and can cause birth eye defects when disrupted. Studying a patient's own cells grown in the laboratory can further help researchers understand how changes in genes affect their function. Both animal and cellular models can be used to develop and test new drugs, which could provide treatment options for patients living with microphthalmia. This review summarises the key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future.
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Affiliation(s)
| | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, 11-43 Bath
Street, London, EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Foundation Trust, London, UK
- The Francis Crick Institute, London, UK
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16
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Darbari E, Zare-Abdollahi D, Alavi A, Rezaei Kanavi M, Feizi S, Hosseini SB, Baradaran-Rafii A, Ahmadieh H, Issazadeh-Navikas S, Elahi E. A mutation in DOP1B identified as a probable cause for autosomal recessive Peters anomaly in a consanguineous family. Mol Vis 2020; 26:757-765. [PMID: 33273802 PMCID: PMC7700884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 11/23/2020] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Peters anomaly (PA) is a heterogeneous developmental disorder characterized by central corneal opacity and iridocorneal or corneolenticular adhesions. Although many causative genes have been identified, most screened patients do not have mutations in the known genes. We aimed to identify the genetic cause of Peters anomaly in a pedigree with three affected individuals. METHODS Slit-lamp biomicroscopy and ultrasound biomicroscopy were performed for definitive diagnosis. Exome sequencing was conducted on the DNA of all three patients. After identification of a candidate causative gene, expression of the gene was assessed with real-time PCR in various ocular tissues of three human embryos and three adults. RESULTS The patients were affected with isolated PA. The parents of the patients were related to one another. Inheritance of PA was autosomal recessive. After appropriate filtering of the exome data, a homozygous variation in DOP1B remained as the only candidate genetic cause of PA in the pedigree. The variant segregated with disease status in the pedigree and was absent among 800 control Iranians. The variant has been reported in various databases at frequencies of 0.006 or less only in the heterozygous state in some cohorts of African origin. The p.Val1660 amino acid affected by the mutation is completely conserved in mammals and birds during evolution. Expression of DOP1B was shown in all adult and embryonic lens, iris, cornea, sclera, and retina tissues that were tested. CONCLUSIONS DOP1B that encodes DOP1 leucine zipper like protein B was identified as the putative PA-causing gene in pedigree PA-101. As DOP1B is positioned within the Down syndrome chromosomal region on chromosome 21, until now this gene has mostly been studied with respect to brain functions. However, members of the Dopey gene family have been shown to have roles in development in other organisms. Evidence of the expression of DOP1B in various PA-relevant eye tissues, which, to the best of our knowledge, is shown here for the first time, is to be noted. However, this finding does not necessarily implicate a specific role for DOP1B in eye development as the gene is expressed in many tissues. Ultimately, definitive assessment of the contribution of DOP1B to PA pathology awaits identification of mutations in the gene in unrelated patients with PA and functional studies.
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Affiliation(s)
- Ensieh Darbari
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Davood Zare-Abdollahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mozhgan Rezaei Kanavi
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sepehr Feizi
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Alireza Baradaran-Rafii
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ahmadieh
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shohreh Issazadeh-Navikas
- Neuroinflammation Unit, Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, Copenhagen Biocentre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Elahe Elahi
- School of Biology, College of Science, University of Tehran, Tehran, Iran
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17
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Fang X, Zhang Y, Cai J, Lu T, Hu J, Yuan F, Chen P. Identification of novel candidate pathogenic genes in pituitary stalk interruption syndrome by whole-exome sequencing. J Cell Mol Med 2020; 24:11703-11717. [PMID: 32864857 PMCID: PMC7579688 DOI: 10.1111/jcmm.15781] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/25/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Pituitary stalk interruption syndrome (PSIS) is a type of congenital malformation of the anterior pituitary, which leads to isolated growth hormone deficiency or multiple hypothalamic-pituitary deficiencies. Many genetic factors have been explored, but they only account for a minority of the genetic aetiology. To identify novel PSIS pathogenic genes, we conducted whole-exome sequencing with 59 sporadic PSIS patients, followed by filtering gene panels involved in pituitary development, holoprosencephaly and midline abnormality. A total of 81 heterozygous variants, distributed among 59 genes, were identified in 50 patients, with 31 patients carrying polygenic variants. Fourteen of the 59 pathogenic genes clustered to the Hedgehog pathway. Of them, PTCH1 and PTCH2, inhibitors of Hedgehog signalling, showed the most frequent heterozygous mutations (22%, seven missense and one frameshift mutations were identified in 13 patients). Moreover, five novel heterozygous null variants in genes including PTCH2 (p.S391fs, combined with p.L104P), Hedgehog acyltransferase (p.R280X, de novo), MAPK3 (p.H50fs), EGR4 (p.G22fs, combined with LHX4 p.S263N) and SPG11 (p.Q1624X), which lead to truncated proteins, were identified. In conclusion, genetic mutations in the Hedgehog signalling pathway might underlie the complex polygenic background of PSIS, and the findings of our study could extend the understanding of PSIS pathogenic genes.
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Affiliation(s)
- Xuqian Fang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuwen Zhang
- Department of Endocrinology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jialin Cai
- Clinical Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingwei Lu
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junjie Hu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Yuan
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peizhan Chen
- Clinical Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Li L, Cui YJ, Zou Y, Yang L, Yin X, Li B, Yan L. Genetic association study of SOX2 gene polymorphisms with high myopia in a Chinese population. Eur J Ophthalmol 2020; 31:734-739. [PMID: 32037877 DOI: 10.1177/1120672120904666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The aim of this study is to investigate whether SOX2 gene variants were associated with high myopia in a Chinese population. METHODS This study is conducted using case-control association analysis. This study recruited 83 healthy controls (with binocular spherical equivalent between -0.50 and +0.50 D) and 117 high myopia cases (spherical equivalent > -6.00 D in both eyes). Three single-nucleotide polymorphisms were selected from HapMap database for genotyping by direct sequencing. Statistical software (SPSS 22.0) was used for statistical analysis. The chi-square test was used to examine the difference in the frequency between cases and controls. RESULTS Genotype distributions in the three single-nucleotide polymorphisms were all in accordance with the Hardy-Weinberg equilibrium. The differences of rs4575941 locus genotype frequency and allele frequency between the case group and the control group were statistically significant (p = .043 and p = .029, respectively). The rs4575941 allele G frequency in the high myopia group was significantly higher than that in the control group with an odds ratio value of 1.579. However, the value of a chi-square test for the trend was 0.029, and after Bonferroni test, the p value was .087. CONCLUSION In Chinese population, rs4575941 in SOX2 gene was likely to play some roles in the genetic susceptibility to high myopia; the rs4575941 allele G might be a risk gene for high myopia.
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Affiliation(s)
- Lan Li
- Department of Ophthalmology, Langzhong People's Hospital, Langzhong, China
| | - Ying Juan Cui
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Yunchun Zou
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong, China
| | - Liyuan Yang
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong, China
| | - Ximin Yin
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong, China
| | - Bo Li
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong, China
| | - Liying Yan
- Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong, China.,Department of Ophthalmology, Suining Central Hospital, Suining, China
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19
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George A, Cogliati T, Brooks BP. Genetics of syndromic ocular coloboma: CHARGE and COACH syndromes. Exp Eye Res 2020; 193:107940. [PMID: 32032630 DOI: 10.1016/j.exer.2020.107940] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023]
Abstract
Optic fissure closure defects result in uveal coloboma, a potentially blinding condition affecting between 0.5 and 2.6 per 10,000 births that may cause up to 10% of childhood blindness. Uveal coloboma is on a phenotypic continuum with microphthalmia (small eye) and anophthalmia (primordial/no ocular tissue), the so-called MAC spectrum. This review gives a brief overview of the developmental biology behind coloboma and its clinical presentation/spectrum. Special attention will be given to two prominent, syndromic forms of coloboma, namely, CHARGE (Coloboma, Heart defect, Atresia choanae, Retarded growth and development, Genital hypoplasia, and Ear anomalies/deafness) and COACH (Cerebellar vermis hypoplasia, Oligophrenia, Ataxia, Coloboma, and Hepatic fibrosis) syndromes. Approaches employed to identify genes involved in optic fissure closure in animal models and recent advances in live imaging of zebrafish eye development are also discussed.
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Affiliation(s)
- Aman George
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Tiziana Cogliati
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA.
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20
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Valensi M, Goldman G, Marchant D, Van Den Berghe L, Jonet L, Daruich A, Robert MP, Krejci E, Klein C, Mascarelli F, Versaux-Botteri C, Moulin A, Putterman M, Guimiot F, Molina T, Terris B, Brémond-Gignac D, Behar-Cohen F, Abitbol MM. Sostdc1 is expressed in all major compartments of developing and adult mammalian eyes. Graefes Arch Clin Exp Ophthalmol 2019; 257:2401-2427. [PMID: 31529323 DOI: 10.1007/s00417-019-04462-4] [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: 04/16/2019] [Revised: 08/20/2019] [Accepted: 09/04/2019] [Indexed: 01/16/2023] Open
Abstract
PURPOSE This study was conducted in order to study Sostdc1 expression in rat and human developing and adult eyes. METHODS Using the yeast signal sequence trap screening method, we identified the Sostdc1 cDNA encoding a protein secreted by the adult rat retinal pigment epithelium. We determined by in situ hybridization, RT-PCR, immunohistochemistry, and western blot analysis Sostdc1 gene and protein expression in developing and postnatal rat ocular tissue sections. We also investigated Sostdc1 immunohistolocalization in developing and adult human ocular tissues. RESULTS We demonstrated a prominent Sostdc1 gene expression in the developing rat central nervous system (CNS) and eyes at early developmental stages from E10.5 days postconception (dpc) to E13 dpc. Specific Sostdc1 immunostaining was also detected in most adult cells of rat ocular tissue sections. We also identified the rat ocular embryonic compartments characterized by a specific Sostdc1 immunohistostaining and specific Pax6, Sox2, Otx2, and Vsx2 immunohistostaining from embryonic stages E10.5 to E13 dpc. Furthermore, we determined the localization of SOSTDC1 immunoreactivity in ocular tissue sections of developing and adult human eyes. Indeed, we detected SOSTDC1 immunostaining in developing and adult human retinal pigment epithelium (RPE) and neural retina (NR) as well as in several developing and adult human ocular compartments, including the walls of choroidal and scleral vessels. Of utmost importance, we observed a strong SOSTDC1 expression in a pathological ocular specimen of type 2 Peters' anomaly complicated by retinal neovascularization as well in the walls ofother pathological extra-ocular vessels. CONCLUSION: As rat Sostdc1 and human SOSTDC1 are dual antagonists of the Wnt/β-catenin and BMP signaling pathways, these results underscore the potential crucial roles of these pathways and their antagonists, such as Sostdc1 and SOSTDC1, in developing and adult mammalian normal eyes as well as in syndromic and nonsyndromic congenital eye diseases.
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Affiliation(s)
- Maud Valensi
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
| | - Gabrielle Goldman
- APHP, Service de Pathologie de L'Hôpital Cochin-Hôtel-Dieu, Université Paris Descartes, 27 rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Dominique Marchant
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
- Sorbonne Paris Cité, UFR SMBH, Laboratoire Hypoxie et poumons, Université Paris 13, EA 2363, 93017, Bobigny, France
| | - Loïc Van Den Berghe
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
- Inserm UMR 1037, CRCT (Cancer Research Center of Toulouse), 31037, Toulouse, France
| | - Laurent Jonet
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
| | - Alejandra Daruich
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
- AP-HP, Hôpital Universitaire Necker-Enfants-Malades, Service d'Ophtalmologie, 149 rue de Sèvres, 75015, Paris, France
| | - Matthieu P Robert
- AP-HP, Hôpital Universitaire Necker-Enfants-Malades, Service d'Ophtalmologie, 149 rue de Sèvres, 75015, Paris, France
- COGnition and Action Group, UMR 8257, CNRS, Université Paris Descartes, Paris, France
| | - Eric Krejci
- COGnition and Action Group, UMR 8257, CNRS, Université Paris Descartes, Paris, France
| | - Christophe Klein
- Centre d'Imagerie Cellulaire et de Cytométrie (CICC), Centre de Recherche des Cordeliers (CRC), Université Pierre et Marie Curie - Paris 6, Université Paris Descartes - Paris 5, UMR_S 1138, 75006, Paris, France
| | - Frédéric Mascarelli
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
| | - Claudine Versaux-Botteri
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
| | - Alexandre Moulin
- Département de Pathologie, Hôpital Ophtalmique Jules-Gonin , 15, avenue de France, 1004, Lausanne, Switzerland
| | - Marc Putterman
- APHP, Service de Pathologie de l'Hôpital Universitaire Necker-Enfants-Malades, Université Paris Descartes, 149 rue de Sèvres, 75015, Paris, France
| | - Fabien Guimiot
- Unité Fonctionnelle de Foeto-Pathologie, Hôpital Universitaire Robert Debré, 48 Boulevard Serrurier, 75019, Paris, France
| | - Thierry Molina
- APHP, Service de Pathologie de l'Hôpital Universitaire Necker-Enfants-Malades, Université Paris Descartes, 149 rue de Sèvres, 75015, Paris, France
| | - Benoît Terris
- APHP, Service de Pathologie de L'Hôpital Cochin-Hôtel-Dieu, Université Paris Descartes, 27 rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Dominique Brémond-Gignac
- AP-HP, Hôpital Universitaire Necker-Enfants-Malades, Service d'Ophtalmologie, 149 rue de Sèvres, 75015, Paris, France
| | - Francine Behar-Cohen
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
- AP-HP, Service d'Ophtalmologie, Hôpital Universitaire Cochin-Hôtel-Dieu, 27 rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Marc M Abitbol
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France.
- AP-HP, Hôpital Universitaire Necker-Enfants-Malades, Service d'Ophtalmologie, 149 rue de Sèvres, 75015, Paris, France.
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21
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Cardozo MJ, Almuedo-Castillo M, Bovolenta P. Patterning the Vertebrate Retina with Morphogenetic Signaling Pathways. Neuroscientist 2019; 26:185-196. [PMID: 31509088 DOI: 10.1177/1073858419874016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The primordium of the vertebrate eye is composed of a pseudostratified and apparently homogeneous neuroepithelium, which folds inward to generate a bilayered optic cup. During these early morphogenetic events, the optic vesicle is patterned along three different axes-proximo-distal, dorso-ventral, and naso-temporal-and three major domains: the neural retina, the retinal pigment epithelium (RPE), and the optic stalk. These fundamental steps that enable the subsequent development of a functional eye, entail the precise coordination among genetic programs. These programs are driven by the interplay of signaling pathways and transcription factors, which progressively dictate how each tissue should evolve. Here, we discuss the contribution of the Hh, Wnt, FGF, and BMP signaling pathways to the early patterning of the retina. Comparative studies in different vertebrate species have shown that their morphogenetic activity is repetitively used to orchestrate the progressive specification of the eye with evolutionary conserved mechanisms that have been adapted to match the specific need of a given species.
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Affiliation(s)
- Marcos J Cardozo
- Centro de Biología Molecular "Severo Ochoa," (CSIC/UAM), Madrid, Spain.,CIBERER, ISCIII, Madrid, Spain
| | | | - Paola Bovolenta
- Centro de Biología Molecular "Severo Ochoa," (CSIC/UAM), Madrid, Spain.,CIBERER, ISCIII, Madrid, Spain
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22
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Holt RJ, Young RM, Crespo B, Ceroni F, Curry CJ, Bellacchio E, Bax DA, Ciolfi A, Simon M, Fagerberg CR, van Binsbergen E, De Luca A, Memo L, Dobyns WB, Mohammed AA, Clokie SJ, Zazo Seco C, Jiang YH, Sørensen KP, Andersen H, Sullivan J, Powis Z, Chassevent A, Smith-Hicks C, Petrovski S, Antoniadi T, Shashi V, Gelb BD, Wilson SW, Gerrelli D, Tartaglia M, Chassaing N, Calvas P, Ragge NK. De Novo Missense Variants in FBXW11 Cause Diverse Developmental Phenotypes Including Brain, Eye, and Digit Anomalies. Am J Hum Genet 2019; 105:640-657. [PMID: 31402090 PMCID: PMC6731360 DOI: 10.1016/j.ajhg.2019.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022] Open
Abstract
The identification of genetic variants implicated in human developmental disorders has been revolutionized by second-generation sequencing combined with international pooling of cases. Here, we describe seven individuals who have diverse yet overlapping developmental anomalies, and who all have de novo missense FBXW11 variants identified by whole exome or whole genome sequencing and not reported in the gnomAD database. Their phenotypes include striking neurodevelopmental, digital, jaw, and eye anomalies, and in one individual, features resembling Noonan syndrome, a condition caused by dysregulated RAS signaling. FBXW11 encodes an F-box protein, part of the Skp1-cullin-F-box (SCF) ubiquitin ligase complex, involved in ubiquitination and proteasomal degradation and thus fundamental to many protein regulatory processes. FBXW11 targets include β-catenin and GLI transcription factors, key mediators of Wnt and Hh signaling, respectively, critical to digital, neurological, and eye development. Structural analyses indicate affected residues cluster at the surface of the loops of the substrate-binding domain of FBXW11, and the variants are predicted to destabilize the protein and/or its interactions. In situ hybridization studies on human and zebrafish embryonic tissues demonstrate FBXW11 is expressed in the developing eye, brain, mandibular processes, and limb buds or pectoral fins. Knockdown of the zebrafish FBXW11 orthologs fbxw11a and fbxw11b resulted in embryos with smaller, misshapen, and underdeveloped eyes and abnormal jaw and pectoral fin development. Our findings support the role of FBXW11 in multiple developmental processes, including those involving the brain, eye, digits, and jaw.
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23
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Harding P, Moosajee M. The Molecular Basis of Human Anophthalmia and Microphthalmia. J Dev Biol 2019; 7:jdb7030016. [PMID: 31416264 PMCID: PMC6787759 DOI: 10.3390/jdb7030016] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
Abstract
Human eye development is coordinated through an extensive network of genetic signalling pathways. Disruption of key regulatory genes in the early stages of eye development can result in aborted eye formation, resulting in an absent eye (anophthalmia) or a small underdeveloped eye (microphthalmia) phenotype. Anophthalmia and microphthalmia (AM) are part of the same clinical spectrum and have high genetic heterogeneity, with >90 identified associated genes. By understanding the roles of these genes in development, including their temporal expression, the phenotypic variation associated with AM can be better understood, improving diagnosis and management. This review describes the genetic and structural basis of eye development, focusing on the function of key genes known to be associated with AM. In addition, we highlight some promising avenues of research involving multiomic approaches and disease modelling with induced pluripotent stem cell (iPSC) technology, which will aid in developing novel therapies.
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Affiliation(s)
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, 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.
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24
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Posbergh CJ, Thonney ML, Huson HJ. Genomic Approaches Identify Novel Gene Associations with Out of Season Lambing in Sheep. J Hered 2019; 110:577-586. [DOI: 10.1093/jhered/esz014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
Abstract
Sheep are seasonally polyestrous, traditionally breeding when the day length shortens in the autumn. The changing photoperiod stimulates reproductive hormones through a series of chemical pathways, ultimately leading to cyclicity. Some breeds of sheep, such as the Polypay and Dorset, have been selected for reduced seasonality and can lamb year-round. Despite this selection, there is still variation within these breeds in the ability to lamb out of season. The identification of out of season lambing quantitative trait loci has the potential to improve genetic progress using genomic selection schemes. Association studies, fixation index (FST), and runs of homozygosity (ROH) were evaluated to identify regions of the genome that influence the ability of ewes to lamb out of season. All analyses used genotypic data from the Illumina Ovine HD beadchip. Genome-wide associations were tested both across breeds in 257 ewes and within the Dorset and Polypay breeds. FST was measured across breeds and between UK and US Dorsets to assess population differences. ROH were estimated in ewes to identify homozygous regions contributing to out of season lambing. Significant associations after multiple testing correction were found through these approaches, leading to the identification of several candidate genes for further study. Genes involved with eye development, reproductive hormones, and neuronal changes were identified as the most promising for influencing the ewe’s ability to lamb year-round. These candidate genes could be advantageous for selection for improved year-round lamb production and provide better insight into the complex regulation of seasonal reproduction.
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Affiliation(s)
| | | | - Heather J Huson
- Department of Animal Science, Cornell University, Ithaca, NY
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25
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Genetics of anophthalmia and microphthalmia. Part 1: Non-syndromic anophthalmia/microphthalmia. Hum Genet 2019; 138:799-830. [PMID: 30762128 DOI: 10.1007/s00439-019-01977-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/30/2019] [Indexed: 12/22/2022]
Abstract
Eye formation is the result of coordinated induction and differentiation processes during embryogenesis. Disruption of any one of these events has the potential to cause ocular growth and structural defects, such as anophthalmia and microphthalmia (A/M). A/M can be isolated or occur with systemic anomalies, when they may form part of a recognizable syndrome. Their etiology includes genetic and environmental factors; several hundred genes involved in ocular development have been identified in humans or animal models. In humans, around 30 genes have been repeatedly implicated in A/M families, although many other genes have been described in single cases or families, and some genetic syndromes include eye anomalies occasionally as part of a wider phenotype. As a result of this broad genetic heterogeneity, with one or two notable exceptions, each gene explains only a small percentage of cases. Given the overlapping phenotypes, these genes can be most efficiently tested on panels or by whole exome/genome sequencing for the purposes of molecular diagnosis. However, despite whole exome/genome testing more than half of patients currently remain without a molecular diagnosis. The proportion of undiagnosed cases is even higher in those individuals with unilateral or milder phenotypes. Furthermore, even when a strong gene candidate is available for a patient, issues of incomplete penetrance and germinal mosaicism make diagnosis and genetic counseling challenging. In this review, we present the main genes implicated in non-syndromic human A/M phenotypes and, for practical purposes, classify them according to the most frequent or predominant phenotype each is associated with. Our intention is that this will allow clinicians to rank and prioritize their molecular analyses and interpretations according to the phenotypes of their patients.
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26
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Zaffran S, Odelin G, Stefanovic S, Lescroart F, Etchevers HC. Ectopic expression of Hoxb1 induces cardiac and craniofacial malformations. Genesis 2018; 56:e23221. [PMID: 30134070 DOI: 10.1002/dvg.23221] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 12/20/2022]
Abstract
Members of the large family of Hox transcription factors are encoded by genes whose tightly regulated expression in development and in space within different embryonic tissues confer positional identity from the neck to the tips of the limbs. Many structures of the face, head, and heart develop from cell populations expressing few or no Hox genes. Hoxb1 is the member of its chromosomal cluster expressed in the most rostral domain during vertebrate development, but never by the multipotent neural crest cell population anterior to the cerebellum. We have developed a novel floxed transgenic mouse line, CAG-Hoxb1,-EGFP (CAG-Hoxb1), which upon recombination by Cre recombinase conditionally induces robust Hoxb1 and eGFP overexpression. When induced within the neural crest lineage, pups die at birth. A variable phenotype develops from E11.5 on, associating frontonasal hypoplasia/aplasia, micrognathia/agnathia, major ocular and forebrain anomalies, and cardiovascular malformations. Neural crest derivatives in the body appear unaffected. Transcription of effectors of developmental signaling pathways (Bmp, Shh, Vegfa) and transcription factors (Pax3, Sox9) is altered in mutants. These outcomes emphasize that repression of Hoxb1, along with other paralog group 1 and 2 Hox genes, is strictly necessary in anterior cephalic NC for craniofacial, visual, auditory, and cardiovascular development.
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Affiliation(s)
| | - Gaëlle Odelin
- Aix Marseille Univ, MMG, INSERM, Marseille, U1251, France
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27
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Slavotinek A. Genetics of anophthalmia and microphthalmia. Part 2: Syndromes associated with anophthalmia-microphthalmia. Hum Genet 2018; 138:831-846. [PMID: 30374660 DOI: 10.1007/s00439-018-1949-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 10/20/2018] [Indexed: 12/12/2022]
Abstract
As new genes for A/M are identified in the genomic era, the number of syndromes associated with A/M has greatly expanded. In this review, we provide a brief synopsis of the clinical presentation and molecular genetic etiology of previously characterized pathways involved in A/M, including the Sex-determining region Y-box 2 (SOX2), Orthodenticle Homeobox 2 (OTX2) and Paired box protein-6 (PAX6) genes, and the Stimulated by retinoic acid gene 6 homolog (STRA6), Aldehyde Dehydrogenase 1 Family Member A3 (ALDH1A3), and RA Receptor Beta (RARβ) genes that are involved in retinoic acid synthesis. Less common genetic causes of A/M, including genes involved in BMP signaling [Bone Morphogenetic Protein 4 (BMP4), Bone Morphogenetic Protein 7 (BMP7) and SPARC-related modular calcium-binding protein 1 (SMOC1)], genes involved in the mitochondrial respiratory chain complex [Holocytochrome c-type synthase (HCCS), Cytochrome C Oxidase Subunit 7B (COX7B), and NADH:Ubiquinone Oxidoreductase subunit B11 (NDUFB11)], the BCL-6 corepressor gene (BCOR), Yes-Associated Protein 1 (YAP1) and Transcription Factor AP-2 Alpha (TFAP2α), are more briefly discussed. We also review several recently described genes and pathways associated with A/M, including Smoothened (SMO) that is involved in Sonic hedgehog (SHH) signaling, Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) and Solute carrier family 25 member 24 (SLC25A24), emphasizing phenotype-genotype correlations and shared pathways where relevant.
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Affiliation(s)
- Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California, San Francisco Room RH384C, 1550 4th St, San Francisco, CA, 94143-2711, USA.
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28
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Cavodeassi F, Creuzet S, Etchevers HC. The hedgehog pathway and ocular developmental anomalies. Hum Genet 2018; 138:917-936. [PMID: 30073412 PMCID: PMC6710239 DOI: 10.1007/s00439-018-1918-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/24/2018] [Indexed: 12/18/2022]
Abstract
Mutations in effectors of the hedgehog signaling pathway are responsible for a wide variety of ocular developmental anomalies. These range from massive malformations of the brain and ocular primordia, not always compatible with postnatal life, to subtle but damaging functional effects on specific eye components. This review will concentrate on the effects and effectors of the major vertebrate hedgehog ligand for eye and brain formation, Sonic hedgehog (SHH), in tissues that constitute the eye directly and also in those tissues that exert indirect influence on eye formation. After a brief overview of human eye development, the many roles of the SHH signaling pathway during both early and later morphogenetic processes in the brain and then eye and periocular primordia will be evoked. Some of the unique molecular biology of this pathway in vertebrates, particularly ciliary signal transduction, will also be broached within this developmental cellular context.
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Affiliation(s)
- Florencia Cavodeassi
- Institute for Medical and Biomedical Education, St. George´s University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Sophie Creuzet
- Institut des Neurosciences Paris-Saclay (Neuro-PSI), UMR 9197, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Heather C Etchevers
- Aix-Marseille Univ, Marseille Medical Genetics (MMG), INSERM, Faculté de Médecine, 27 boulevard Jean Moulin, 13005, Marseille, France.
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29
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Zheng SS, Han RY, Xiang L, Zhuang YY, Jin ZB. Versatile Genome Engineering Techniques Advance Human Ocular Disease Researches in Zebrafish. Front Cell Dev Biol 2018; 6:75. [PMID: 30050903 PMCID: PMC6052052 DOI: 10.3389/fcell.2018.00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
Abstract
Over recent decades, zebrafish has been established as a sophisticated vertebrate model for studying human ocular diseases due to its high fecundity, short generation time and genetic tractability. With the invention of morpholino (MO) technology, it became possible to study the genetic basis and relevant genes of ocular diseases in vivo. Many genes have been shown to be related to ocular diseases. However, the issue of specificity is the major concern in defining gene functions with MO technology. The emergence of the first- and second-generation genetic modification tools zinc-finger nucleases (ZFNs) and TAL effector nucleases (TALENs), respectively, eliminated the potential phenotypic risk induced by MOs. Nevertheless, the efficiency of these nucleases remained relatively low until the third technique, the clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, was discovered. This review highlights the application of multiple genome engineering techniques, especially the CRISPR/Cas9 system, in the study of human ocular diseases in zebrafish.
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Affiliation(s)
- Si-Si Zheng
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Ru-Yi Han
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Lue Xiang
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - You-Yuan Zhuang
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
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30
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Gielen RJCAM, Reinders MGHC, Koillinen HK, Paulussen ADC, Mosterd K, van Geel M. PTCH1 isoform 1b is the major transcript in the development of basal cell nevus syndrome. J Hum Genet 2018; 63:965-969. [DOI: 10.1038/s10038-018-0485-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 01/07/2023]
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31
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Cela P, Hampl M, Shylo NA, Christopher KJ, Kavkova M, Landova M, Zikmund T, Weatherbee SD, Kaiser J, Buchtova M. Ciliopathy Protein Tmem107 Plays Multiple Roles in Craniofacial Development. J Dent Res 2017; 97:108-117. [PMID: 28954202 DOI: 10.1177/0022034517732538] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A broad spectrum of human diseases called ciliopathies is caused by defective primary cilia morphology or signal transduction. The primary cilium is a solitary organelle that responds to mechanical and chemical stimuli from extracellular and intracellular environments. Transmembrane protein 107 (TMEM107) is localized in the primary cilium and is enriched at the transition zone where it acts to regulate protein content of the cilium. Mutations in TMEM107 were previously connected with oral-facial-digital syndrome, Meckel-Gruber syndrome, and Joubert syndrome exhibiting a range of ciliopathic defects. Here, we analyze a role of Tmem107 in craniofacial development with special focus on palate formation, using mouse embryos with a complete knockout of Tmem107. Tmem107-/- mice were affected by a broad spectrum of craniofacial defects, including shorter snout, expansion of the facial midline, cleft lip, extensive exencephaly, and microphthalmia or anophthalmia. External abnormalities were accompanied by defects in skeletal structures, including ossification delay in several membranous bones and enlargement of the nasal septum or defects in vomeronasal cartilage. Alteration in palatal shelves growth resulted in clefting of the secondary palate. Palatal defects were caused by increased mesenchymal proliferation leading to early overgrowth of palatal shelves followed by defects in their horizontalization. Moreover, the expression of epithelial stemness marker SOX2 was altered in the palatal shelves of Tmem107-/- animals, and differences in mesenchymal SOX9 expression demonstrated the enhancement of neural crest migration. Detailed analysis of primary cilia revealed region-specific changes in ciliary morphology accompanied by alteration of acetylated tubulin and IFT88 expression. Moreover, Shh and Gli1 expression was increased in Tmem107-/- animals as shown by in situ hybridization. Thus, TMEM107 is essential for proper head development, and defective TMEM107 function leads to ciliary morphology disruptions in a region-specific manner, which may explain the complex mutant phenotype.
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Affiliation(s)
- P Cela
- 1 Institute of Animal Physiology and Genetics, CAS, Brno, Czech Republic.,2 Department of Physiology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - M Hampl
- 1 Institute of Animal Physiology and Genetics, CAS, Brno, Czech Republic.,3 Department of Experimental Biology, Faculty of Sciences, Masaryk University, Brno, Czech Republic
| | - N A Shylo
- 4 Department of Genetics, Yale University, School of Medicine, New Haven, CT, USA
| | - K J Christopher
- 4 Department of Genetics, Yale University, School of Medicine, New Haven, CT, USA
| | - M Kavkova
- 5 CEITEC-Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - M Landova
- 1 Institute of Animal Physiology and Genetics, CAS, Brno, Czech Republic.,3 Department of Experimental Biology, Faculty of Sciences, Masaryk University, Brno, Czech Republic
| | - T Zikmund
- 5 CEITEC-Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - S D Weatherbee
- 4 Department of Genetics, Yale University, School of Medicine, New Haven, CT, USA
| | - J Kaiser
- 5 CEITEC-Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - M Buchtova
- 1 Institute of Animal Physiology and Genetics, CAS, Brno, Czech Republic.,3 Department of Experimental Biology, Faculty of Sciences, Masaryk University, Brno, Czech Republic
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32
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Wiel L, Venselaar H, Veltman JA, Vriend G, Gilissen C. Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. Hum Mutat 2017; 38:1454-1463. [PMID: 28815929 PMCID: PMC5656839 DOI: 10.1002/humu.23313] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 12/11/2022]
Abstract
Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population‐based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease‐causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 “meta‐domains.” These meta‐domains consist of 30,853 homologous Pfam protein domain instances that cover 36% of all human protein coding sequences. We find that genetic tolerance is consistent across protein domain homologues, and that patterns of genetic tolerance faithfully mimic patterns of evolutionary conservation. Furthermore, for a significant fraction (68%) of the meta‐domains high‐frequency population variation re‐occurs at the same positions across domain homologues more often than expected. In addition, we observe that the presence of pathogenic missense variants at an aligned homologous domain position is often paired with the absence of population variation and vice versa. The use of these meta‐domains can improve the interpretation of genetic variation.
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
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33
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Riera M, Wert A, Nieto I, Pomares E. Panel-based whole exome sequencing identifies novel mutations in microphthalmia and anophthalmia patients showing complex Mendelian inheritance patterns. Mol Genet Genomic Med 2017; 5:709-719. [PMID: 29178648 PMCID: PMC5702572 DOI: 10.1002/mgg3.329] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/21/2017] [Accepted: 07/27/2017] [Indexed: 12/15/2022] Open
Abstract
Background Microphthalmia and anophthalmia (MA) are congenital eye abnormalities that show an extremely high clinical and genetic complexity. In this study, we evaluated the implementation of whole exome sequencing (WES) for the genetic analysis of MA patients. This approach was used to investigate three unrelated families in which previous single‐gene analyses failed to identify the molecular cause. Methods A total of 47 genes previously associated with nonsyndromic MA were included in our panel. WES was performed in one affected patient from each family using the AmpliSeqTM Exome technology and the Ion ProtonTM platform. Results A novel heterozygous OTX2 missense mutation was identified in a patient showing bilateral anophthalmia who inherited the variant from a parent who was a carrier, but showed no sign of the condition. We also describe a new PAX6 missense variant in an autosomal‐dominant pedigree affected by mild bilateral microphthalmia showing high intrafamiliar variability, with germline mosaicism determined to be the most plausible molecular cause of the disease. Finally, a heterozygous missense mutation in RBP4 was found to be responsible in an isolated case of bilateral complex microphthalmia. Conclusion This study highlights that panel‐based WES is a reliable and effective strategy for the genetic diagnosis of MA. Furthermore, using this technique, the mutational spectrum of these diseases was broadened, with novel variants identified in each of the OTX2,PAX6, and RBP4 genes. Moreover, we report new cases of reduced penetrance, mosaicism, and variable phenotypic expressivity associated with MA, further demonstrating the heterogeneity of such disorders.
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Affiliation(s)
- Marina Riera
- Departament de Genètica, Institut de Microcirurgia Ocular (IMO), Barcelona, Spain
| | - Ana Wert
- Departament d'Oftalmologia Pediàtrica, Estrabisme i Neuroftalmologia, Institut de Microcirurgia Ocular (IMO), Barcelona, Spain
| | - Isabel Nieto
- Departament de Còrnia, Cataracta i Cirurgia Refractiva, Institut de Microcirurgia Ocular (IMO), Barcelona, Spain
| | - Esther Pomares
- Departament de Genètica, Institut de Microcirurgia Ocular (IMO), Barcelona, Spain
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34
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Shaw ND, Brand H, Kupchinsky ZA, Bengani H, Plummer L, Jones TI, Erdin S, Williamson KA, Rainger J, Stortchevoi A, Samocha K, Currall BB, Dunican DS, Collins RL, Willer JR, Lek A, Lek M, Nassan M, Pereira S, Kammin T, Lucente D, Silva A, Seabra CM, Chiang C, An Y, Ansari M, Rainger JK, Joss S, Smith JC, Lippincott MF, Singh SS, Patel N, Jing JW, Law JR, Ferraro N, Verloes A, Rauch A, Steindl K, Zweier M, Scheer I, Sato D, Okamoto N, Jacobsen C, Tryggestad J, Chernausek S, Schimmenti LA, Brasseur B, Cesaretti C, García-Ortiz JE, Buitrago TP, Silva OP, Hoffman JD, Mühlbauer W, Ruprecht KW, Loeys BL, Shino M, Kaindl AM, Cho CH, Morton CC, Meehan RR, van Heyningen V, Liao EC, Balasubramanian R, Hall JE, Seminara SB, Macarthur D, Moore SA, Yoshiura KI, Gusella JF, Marsh JA, Graham JM, Lin AE, Katsanis N, Jones PL, Crowley WF, Davis EE, FitzPatrick DR, Talkowski ME. SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome. Nat Genet 2017; 49:238-248. [PMID: 28067909 PMCID: PMC5473428 DOI: 10.1038/ng.3743] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022]
Abstract
Arhinia, or absence of the nose, is a rare malformation of unknown etiology that is often accompanied by ocular and reproductive defects. Sequencing of 40 people with arhinia revealed that 84% of probands harbor a missense mutation localized to a constrained region of SMCHD1 encompassing the ATPase domain. SMCHD1 mutations cause facioscapulohumeral muscular dystrophy type 2 (FSHD2) via a trans-acting loss-of-function epigenetic mechanism. We discovered shared mutations and comparable DNA hypomethylation patterning between these distinct disorders. CRISPR/Cas9-mediated alteration of smchd1 in zebrafish yielded arhinia-relevant phenotypes. Transcriptome and protein analyses in arhinia probands and controls showed no differences in SMCHD1 mRNA or protein abundance but revealed regulatory changes in genes and pathways associated with craniofacial patterning. Mutations in SMCHD1 thus contribute to distinct phenotypic spectra, from craniofacial malformation and reproductive disorders to muscular dystrophy, which we speculate to be consistent with oligogenic mechanisms resulting in pleiotropic outcomes.
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Affiliation(s)
- Natalie D Shaw
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Harrison Brand
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Zachary A Kupchinsky
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - Hemant Bengani
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Lacey Plummer
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Takako I Jones
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Serkan Erdin
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kathleen A Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Joe Rainger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kaitlin Samocha
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin B Currall
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Donncha S Dunican
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Ryan L Collins
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason R Willer
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - Angela Lek
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Malik Nassan
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA
| | - Shahrin Pereira
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tammy Kammin
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexandra Silva
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Catarina M Seabra
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- GABBA Program, University of Porto, Porto, Portugal
| | - Colby Chiang
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yu An
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Morad Ansari
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Jacqueline K Rainger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Shelagh Joss
- West of Scotland Genetics Service, South Glasgow University Hospitals, Glasgow, UK
| | - Jill Clayton Smith
- Faculty of Medical and Human Sciences, Institute of Human Development, Manchester Centre for Genomic Medicine, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Margaret F Lippincott
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sylvia S Singh
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Nirav Patel
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jenny W Jing
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jennifer R Law
- Division of Pediatric Endocrinology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nalton Ferraro
- Department of Oral and Maxillofacial Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alain Verloes
- Department of Genetics, Robert Debré Hospital, Paris, France
| | - Anita Rauch
- Institute of Medical Genetics and Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics and Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Schlieren-Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics and Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Schlieren-Zurich, Switzerland
| | - Ianina Scheer
- Department of Diagnostic Imaging, Children's Hospital, Zurich, Switzerland
| | - Daisuke Sato
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Christina Jacobsen
- Division of Endocrinology and Genetics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jeanie Tryggestad
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Steven Chernausek
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Lisa A Schimmenti
- Departments of Otorhinolaryngology and Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Benjamin Brasseur
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Claudia Cesaretti
- Medical Genetics Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Jose E García-Ortiz
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | | | | | - Jodi D Hoffman
- Divisions of Genetics and Maternal Fetal Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Wolfgang Mühlbauer
- Department of Plastic and Aesthetic Surgery, ATOS Klinik, Munich, Germany
| | - Klaus W Ruprecht
- Department of Ophthalmology, University Hospital of the Saarland, Homburg, Germany
| | - Bart L Loeys
- Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Masato Shino
- Department of Otolaryngology and Head and Neck Surgery, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Angela M Kaindl
- Biology and Neurobiology, Charité-University Medicine Berlin and Berlin Institute of Health, Berlin, Germany
| | - Chie-Hee Cho
- Department of Diagnostic, Interventional and Pediatric Radiology, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Cynthia C Morton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Eric C Liao
- Center for Regenerative Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Ravikumar Balasubramanian
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Janet E Hall
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Stephanie B Seminara
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel Macarthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A Moore
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - James F Gusella
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - John M Graham
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Angela E Lin
- Medical Genetics, MassGeneral Hospital for Children and Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - Peter L Jones
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - William F Crowley
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Michael E Talkowski
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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35
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Richieri-Costa A, Vendramini-Pittoli S, Kokitsu-Nakata NM, Zechi-Ceide RM, Alvarez CW, Ribeiro-Bicudo LA. Multisystem Involvement in a Patient with a PTCH1 Mutation: Clinical and Imaging Findings. J Pediatr Genet 2016; 6:103-106. [PMID: 28496998 DOI: 10.1055/s-0036-1588028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/21/2016] [Indexed: 10/21/2022]
Abstract
In this article, we report on a Brazilian female patient born to consanguineous parents and presenting with alobar holoprosencephaly, severe eye involvement, and unusual skin hyperpigmented lesions. She was found to have a mutation (c.2240T > C; p.Val751Gly) in exon 15 of the PTCH1 gene. Mutations in this gene are associated with the nevoid basal cell carcinoma syndrome (NBCCS, OMIM 109400) and, in other instances, with holoprosencephaly (holoprosencephaly-7, OMIM 610828). Severe eye involvement ranging from orbital coloboma to microphthalmia has been seldom reported in patients with NBCCS with PTCH1 mutations. To our knowledge, this is the first report of an individual with central nervous system, skin, and eye manifestations due to a PTCH1 mutation. Mechanisms involved in these multisystem manifestations are discussed.
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Affiliation(s)
- Antonio Richieri-Costa
- Serviço de Genética, Hospital de Reabilitação de Anomalias Craniofaciais, Universidade de São Paulo, Bauru, Sao Paulo, Brazil
| | - Siulan Vendramini-Pittoli
- Serviço de Genética, Hospital de Reabilitação de Anomalias Craniofaciais, Universidade de São Paulo, Bauru, Sao Paulo, Brazil
| | - Nancy Mizue Kokitsu-Nakata
- Serviço de Genética, Hospital de Reabilitação de Anomalias Craniofaciais, Universidade de São Paulo, Bauru, Sao Paulo, Brazil
| | - Roseli Maria Zechi-Ceide
- Serviço de Genética, Hospital de Reabilitação de Anomalias Craniofaciais, Universidade de São Paulo, Bauru, Sao Paulo, Brazil
| | - Camila Wenceslau Alvarez
- Serviço de Genética, Hospital de Reabilitação de Anomalias Craniofaciais, Universidade de São Paulo, Bauru, Sao Paulo, Brazil
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