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Li J, Yang W, Wang YJ, Ma C, Curry CJ, McGoldrick D, Nickerson DA, Chong JX, Blue EE, Mullikin JC, Reefhuis J, Nembhard WN, Romitti PA, Werler MM, Browne ML, Olshan AF, Finnell RH, Feldkamp ML, Pangilinan F, Almli LM, Bamshad MJ, Brody LC, Jenkins MM, Shaw GM. Exome sequencing identifies genetic variants in anophthalmia and microphthalmia. Am J Med Genet A 2022; 188:2376-2388. [PMID: 35716026 PMCID: PMC9283271 DOI: 10.1002/ajmg.a.62874] [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: 11/09/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/10/2022]
Abstract
Anophthalmia and microphthalmia (A/M) are rare birth defects affecting up to 2 per 10,000 live births. These conditions are manifested by the absence of an eye or reduced eye volumes within the orbit leading to vision loss. Although clinical case series suggest a strong genetic component in A/M, few systematic investigations have been conducted on potential genetic contributions owing to low population prevalence. To overcome this challenge, we utilized DNA samples and data collected as part of the National Birth Defects Prevention Study (NBDPS). The NBDPS employed multi-center ascertainment of infants affected by A/M. We performed exome sequencing on 67 family trios and identified numerous genes affected by rare deleterious nonsense and missense variants in this cohort, including de novo variants. We identified 9 nonsense changes and 86 missense variants that are absent from the reference human population (Genome Aggregation Database), and we suggest that these are high priority candidate genes for A/M. We also performed literature curation, single cell transcriptome comparisons, and molecular pathway analysis on the candidate genes and performed protein structure modeling to determine the potential pathogenic variant consequences on PAX6 in this disease.
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Affiliation(s)
- Jingjing Li
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, the Bakar Computational Health Sciences Institute, the Parker Institute for Cancer Immunotherapy, and the Department of Neurology, School of Medicine, University of California, San Francisco, CA, USA
| | - Wei Yang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuejun Jessie Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, the Bakar Computational Health Sciences Institute, the Parker Institute for Cancer Immunotherapy, and the Department of Neurology, School of Medicine, University of California, San Francisco, CA, USA
| | - Chen Ma
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Cynthia J. Curry
- Genetic Medicine, Department of Pediatrics, University of California, San Francisco/Fresno, CA, USA
| | - Daniel McGoldrick
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Elizabeth E. Blue
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - James C. Mullikin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennita Reefhuis
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Wendy N. Nembhard
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Paul A. Romitti
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, USA
| | - Martha M. Werler
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Marilyn L. Browne
- Birth Defects Registry, New York State Department of Health, Albany, NY, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, NY, USA
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard H. Finnell
- Center for Precision Environmental Health, Departments of Molecular and Cellular Biology, Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Marcia L. Feldkamp
- Division of Medical Genetics, Department of Pediatrics, 295 Chipeta Way, Suite 2S010, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Faith Pangilinan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lynn M. Almli
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mike J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Lawrence C. Brody
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary M. Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
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Zhang W, Frausto R, Chung DD, Griffis CG, Kao L, Chen A, Azimov R, Sampath AP, Kurtz I, Aldave AJ. Energy Shortage in Human and Mouse Models of SLC4A11-Associated Corneal Endothelial Dystrophies. Invest Ophthalmol Vis Sci 2021; 61:39. [PMID: 32721020 PMCID: PMC7425690 DOI: 10.1167/iovs.61.8.39] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose To elucidate the molecular events in solute carrier family 4 member 11 (SLC4A11)-deficient corneal endothelium that lead to the endothelial dysfunction that characterizes the dystrophies associated with SLC4A11 mutations, congenital hereditary endothelial dystrophy (CHED) and Fuchs endothelial corneal dystrophy 4. Methods Comparative transcriptomic analysis (CTA) was performed in primary human corneal endothelial cells (pHCEnC) and murine corneal endothelial cells (MCEnC) with normal and reduced levels of SLC4A11 (SLC4A11 KD pHCEnC) and Slc4a11 (Slc4a11−/− MCEnC), respectively. Validation of differentially expressed genes was performed using immunofluorescence staining of CHED corneal endothelium, as well as western blot and quantitative PCR analysis of SLC4A11 KD pHCEnC and Slc4a11−/− MCEnC. Functional analyses were performed to investigate potential functional changes associated with the observed transcriptomic alterations. Results CTA revealed inhibition of cell metabolism and ion transport function as well as mitochondrial dysfunction, leading to reduced adenosine triphosphate (ATP) production, in SLC4A11 KD pHCEnC and Slc4a11−/− MCEnC. Co-localization of SNARE protein STX17 with mitochondria marker COX4 was observed in CHED corneal endothelium, as was activation of AMPK–p53/ULK1 in both SLC4A11 KD pHCEnC and Slc4a11−/− MCEnC, providing additional evidence of mitochondrial dysfunction and mitophagy. Reduced Na+-dependent HCO3− transport activity and altered NH4Cl-induced membrane potential changes were observed in Slc4a11−/− MCEnC. Conclusions Reduced steady-state ATP levels and subsequent activation of the AMPK–p53 pathway provide a link between the metabolic functional deficit and transcriptome alterations, as well as evidence of insufficient ATP to maintain the Na+/K+-ATPase corneal endothelial pump as the cause of the edema that characterizes SLC4A11-associated corneal endothelial dystrophies.
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Takahashi D, Mori T, Sohara E, Tanaka M, Chiga M, Inoue Y, Nomura N, Zeniya M, Ochi H, Takeda S, Suganami T, Rai T, Uchida S. WNK4 is an Adipogenic Factor and Its Deletion Reduces Diet-Induced Obesity in Mice. EBioMedicine 2017; 18:118-127. [PMID: 28314693 PMCID: PMC5405161 DOI: 10.1016/j.ebiom.2017.03.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 02/27/2017] [Accepted: 03/07/2017] [Indexed: 11/25/2022] Open
Abstract
The with-no-lysine kinase (WNK) 4 gene is a causative gene in pseudohypoaldosteronism type II. Although WNKs are widely expressed in the body, neither their metabolic functions nor their extrarenal role is clear. In this study, we found that WNK4 was expressed in mouse adipose tissue and 3T3-L1 adipocytes. In mouse primary preadipocytes and in 3T3-L1 adipocytes, WNK4 was markedly induced in the early phase of adipocyte differentiation. WNK4 expression preceded the expression of key transcriptional factors PPARγ and C/EBPα. WNK4-siRNA-transfected 3T3-L1 cells and human mesenchymal stem cells showed reduced expression of PPARγ and C/EBPα and lipid accumulation. WNK4 protein affected the DNA-binding ability of C/EBPβ and thereby reduced PPARγ expression. In the WNK4−/− mice, PPARγ and C/EBPα expression were decreased in adipose tissues, and the mice exhibited partial resistance to high-fat diet-induced adiposity. These data suggest that WNK4 may be a proadipogenic factor, and offer insights into the relationship between WNKs and energy metabolism. WNK4 regulates adipocyte differentiation in mouse and human preadipocytes. WNK4−/− mice exhibit reduced adiposity and increased insulin sensitivity. WNK4 may be a drug target for diet-induced obesity and salt-sensitive hypertension.
The with-no-lysine kinase (WNK) 4 gene is a causative gene in pseudohypoaldosteronism type II, a hereditary hypertensive disease. Although WNKs are widely expressed in the body and are involved in the pathogenesis of hypertension, neither their metabolic functions nor their extrarenal role is clear. This study demonstrated a contribution of WNK4 to the regulation of core transcriptional factors for adipogenesis and that its depletion indicates some beneficial effects for obesity by a high-fat diet. This study suggests a role of hypertension-causing WNK4 as a proadipogenic factor and offers insights into the relationship between WNKs and energy metabolism.
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Affiliation(s)
- Daiei Takahashi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Miyako Tanaka
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Motoko Chiga
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Yuichi Inoue
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Naohiro Nomura
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Moko Zeniya
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Hiroki Ochi
- Department of Physiology and Cell Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Shu Takeda
- Department of Physiology and Cell Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Takayoshi Suganami
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Tatemitsu Rai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan..
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Goto T, Matsuzawa J, Iemura SI, Natsume T, Shibuya H. WDR26 is a new partner of Axin1 in the canonical Wnt signaling pathway. FEBS Lett 2016; 590:1291-303. [PMID: 27098453 PMCID: PMC5084729 DOI: 10.1002/1873-3468.12180] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/25/2016] [Accepted: 04/05/2016] [Indexed: 01/19/2023]
Abstract
The stability of β‐catenin is very important for canonical Wnt signaling. A protein complex including Axin/APC/GSK3β phosphorylates β‐catenin to be degraded by ubiquitination with β‐TrCP. In the recent study, we isolated WDR26, a protein that binds to Axin. Here, we found that WDR26 is a negative regulator of the canonical Wnt signaling pathway, and that WDR26 affected β‐catenin levels. In addition, WDR26/Axin binding is involved in the ubiquitination of β‐catenin. These results suggest that WDR26 plays a negative role in β‐catenin degradation in the Wnt signaling pathway.
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Affiliation(s)
- Toshiyasu Goto
- Department of Molecular Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Japan
| | - Junhei Matsuzawa
- Department of Molecular Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Japan
| | - Shun-Ichiro Iemura
- Molecular Profiling Research Center for Drug Discovery, National Institutes of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institutes of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Hiroshi Shibuya
- Department of Molecular Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Japan
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Luehders K, Sasai N, Davaapil H, Kurosawa-Yoshida M, Hiura H, Brah T, Ohnuma SI. The small leucine-rich repeat secreted protein Asporin induces eyes in Xenopus embryos through the IGF signalling pathway. Development 2016; 142:3351-61. [PMID: 26443635 DOI: 10.1242/dev.124438] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Small leucine-rich repeat proteoglycan (SLRP) family proteins play important roles in a number of biological events. Here, we demonstrate that the SLRP family member Asporin (ASPN) plays a crucial role in the early stages of eye development in Xenopus embryos. During embryogenesis, ASPN is broadly expressed in the neuroectoderm of the embryo. Overexpression of ASPN causes the induction of ectopic eyes. By contrast, blocking ASPN function with a morpholino oligonucleotide (ASPN-MO) inhibits eye formation, indicating that ASPN is an essential factor for eye development. Detailed molecular analyses revealed that ASPN interacts with insulin growth factor receptor (IGFR) and is essential for activating the IGF receptor-mediated intracellular signalling pathway. Moreover, ASPN perturbed the Wnt, BMP and Activin signalling pathways, suggesting that ASPN thereby creates a favourable environment in which the IGF signal can dominate. ASPN is thus a novel secreted molecule essential for eye induction through the coordination of multiple signalling pathways.
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Affiliation(s)
- Kristin Luehders
- Ocular Biology and Therapeutic unit (ORBIT), Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Noriaki Sasai
- Ocular Biology and Therapeutic unit (ORBIT), Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK Developmental Biomedical Science, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama-cho, Ikoma 630-0192, Japan
| | - Hongorzul Davaapil
- Ocular Biology and Therapeutic unit (ORBIT), Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Maiko Kurosawa-Yoshida
- Department of Oncology, The Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK
| | - Hitoshi Hiura
- Ocular Biology and Therapeutic unit (ORBIT), Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Tara Brah
- Ocular Biology and Therapeutic unit (ORBIT), Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Shin-ichi Ohnuma
- Ocular Biology and Therapeutic unit (ORBIT), Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK Department of Oncology, The Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK
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