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Ishikawa Y, Bonna A, Gould DB, Farndale RW. Local Net Charge State of Collagen Triple Helix Is a Determinant of FKBP22 Binding to Collagen III. Int J Mol Sci 2023; 24:15156. [PMID: 37894834 PMCID: PMC10607241 DOI: 10.3390/ijms242015156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Mutations in the FKBP14 gene encoding the endoplasmic reticulum resident collagen-related proline isomerase FK506 binding protein 22 kDa (FKBP22) result in kyphoscoliotic Ehlers-Danlos Syndrome (EDS), which is characterized by a broad phenotypic outcome. A plausible explanation for this outcome is that FKBP22 participates in the biosynthesis of subsets of collagen types: FKBP22 selectively binds to collagens III, IV, VI, and X, but not to collagens I, II, V, and XI. However, these binding mechanisms have never been explored, and they may underpin EDS subtype heterogeneity. Here, we used collagen Toolkit peptide libraries to investigate binding specificity. We observed that FKBP22 binding was distributed along the collagen helix. Further, it (1) was higher on collagen III than collagen II peptides and it (2) was correlated with a positive peptide charge. These findings begin to elucidate the mechanism by which FKBP22 interacts with collagen.
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Affiliation(s)
- Yoshihiro Ishikawa
- Department of Ophthalmology, University of California San Francisco, School of Medicine, San Francisco, CA 941583, USA
| | - Arkadiusz Bonna
- Department of Biochemistry, Downing Site, Cambridge CB2 1QW, UK
| | - Douglas B. Gould
- Department of Ophthalmology, University of California San Francisco, School of Medicine, San Francisco, CA 941583, USA
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
- Bakar Aging Research Institute, University of California, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, CA 94143, USA
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Colman M, Vroman R, Dhooge T, Malfait Z, Symoens S, Burnyté B, Nampoothiri S, Kariminejad A, Malfait F, Syx D. Kyphoscoliotic Ehlers-Danlos syndrome caused by pathogenic variants in FKBP14: Further insights into the phenotypic spectrum and pathogenic mechanisms. Hum Mutat 2022; 43:1994-2009. [PMID: 36054293 DOI: 10.1002/humu.24456] [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: 02/21/2022] [Revised: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 01/25/2023]
Abstract
The Ehlers-Danlos syndromes (EDS) are a heterogeneous group of heritable connective tissue diseases. The autosomal recessive kyphoscoliotic EDS results from deficiency of either lysyl hydroxylase 1 (encoded by PLOD1), crucial for collagen cross-linking; or the peptidyl-prolyl cis-trans isomerase family FK506-binding protein 22 kDa (FKBP22 encoded by FKBP14), a molecular chaperone of types III, IV, VI, and X collagen. This study reports the clinical manifestations of three probands with homozygous pathogenic FKBP14 variants, including the previously reported c.362dupC; p.(Glu122Argfs*7) variant, a novel missense variant (c.587A>G; p.(Asp196Gly)) and a start codon variant (c.2T>G; p.?). Consistent clinical features in the hitherto reported individuals (n = 40) are kyphoscoliosis, generalized joint hypermobility and congenital muscle hypotonia. Severe vascular complications have been observed in 12.5%. A previously unreported feature is microcornea observed in two probands reported here. Both the c.587A>G and the c.362dupC variant cause complete loss of FKBP22. With immunocytochemistry on dermal fibroblasts, we provide the first evidence for intracellular retention of types III and VI collagen in EDS-FKBP14. Scratch wound assays were largely normal. Western blot of proteins involved in the unfolded protein response and autophagy did not reveal significant upregulation in dermal fibroblasts.
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Affiliation(s)
- Marlies Colman
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Robin Vroman
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Tibbe Dhooge
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Zoë Malfait
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Sofie Symoens
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Biruté Burnyté
- Center for Medical Genetics, Vilnius University Hospital Santariskiu Klinikos, Vilnius, Lithuania
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Kerala, India
| | | | - Fransiska Malfait
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Delfien Syx
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
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Dahary D, Golan Y, Mazor Y, Zelig O, Barshir R, Twik M, Iny Stein T, Rosner G, Kariv R, Chen F, Zhang Q, Shen Y, Safran M, Lancet D, Fishilevich S. Genome analysis and knowledge-driven variant interpretation with TGex. BMC Med Genomics 2019; 12:200. [PMID: 31888639 PMCID: PMC6937949 DOI: 10.1186/s12920-019-0647-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/15/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The clinical genetics revolution ushers in great opportunities, accompanied by significant challenges. The fundamental mission in clinical genetics is to analyze genomes, and to identify the most relevant genetic variations underlying a patient's phenotypes and symptoms. The adoption of Whole Genome Sequencing requires novel capacities for interpretation of non-coding variants. RESULTS We present TGex, the Translational Genomics expert, a novel genome variation analysis and interpretation platform, with remarkable exome analysis capacities and a pioneering approach of non-coding variants interpretation. TGex's main strength is combining state-of-the-art variant filtering with knowledge-driven analysis made possible by VarElect, our highly effective gene-phenotype interpretation tool. VarElect leverages the widely used GeneCards knowledgebase, which integrates information from > 150 automatically-mined data sources. Access to such a comprehensive data compendium also facilitates TGex's broad variant annotation, supporting evidence exploration, and decision making. TGex has an interactive, user-friendly, and easy adaptive interface, ACMG compliance, and an automated reporting system. Beyond comprehensive whole exome sequence capabilities, TGex encompasses innovative non-coding variants interpretation, towards the goal of maximal exploitation of whole genome sequence analyses in the clinical genetics practice. This is enabled by GeneCards' recently developed GeneHancer, a novel integrative and fully annotated database of human enhancers and promoters. Examining use-cases from a variety of TGex users world-wide, we demonstrate its high diagnostic yields (42% for single exome and 50% for trios in 1500 rare genetic disease cases) and critical actionable genetic findings. The platform's support for integration with EHR and LIMS through dedicated APIs facilitates automated retrieval of patient data for TGex's customizable reporting engine, establishing a rapid and cost-effective workflow for an entire range of clinical genetic testing, including rare disorders, cancer predisposition, tumor biopsies and health screening. CONCLUSIONS TGex is an innovative tool for the annotation, analysis and prioritization of coding and non-coding genomic variants. It provides access to an extensive knowledgebase of genomic annotations, with intuitive and flexible configuration options, allows quick adaptation, and addresses various workflow requirements. It thus simplifies and accelerates variant interpretation in clinical genetics workflows, with remarkable diagnostic yield, as exemplified in the described use cases. TGex is available at http://tgex.genecards.org/.
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Affiliation(s)
- Dvir Dahary
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA.
| | - Yaron Golan
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA
| | - Yaron Mazor
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA
| | - Ofer Zelig
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA
| | - Ruth Barshir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Rosner
- Department of Gastroenterology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Revital Kariv
- Department of Gastroenterology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Fei Chen
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Qiang Zhang
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Yiping Shen
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China.,Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.,Department of Neurology, Harvard Medical School, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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