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Cheng YHH, Bohaczuk SC, Stergachis AB. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum Genet 2024; 143:559-605. [PMID: 38436667 PMCID: PMC11078748 DOI: 10.1007/s00439-023-02639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.
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Affiliation(s)
- Y H Hank Cheng
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C Bohaczuk
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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Panzaru MC, Florea A, Caba L, Gorduza EV. Classification of osteogenesis imperfecta: Importance for prophylaxis and genetic counseling. World J Clin Cases 2023; 11:2604-2620. [PMID: 37214584 PMCID: PMC10198117 DOI: 10.12998/wjcc.v11.i12.2604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/18/2023] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Osteogenesis imperfecta (OI) is a genetically heterogeneous monogenic disease characterized by decreased bone mass, bone fragility, and recurrent fractures. The phenotypic spectrum varies considerably ranging from prenatal fractures with lethal outcomes to mild forms with few fractures and normal stature. The basic mechanism is a collagen-related defect, not only in synthesis but also in folding, processing, bone mineralization, or osteoblast function. In recent years, great progress has been made in identifying new genes and molecular mechanisms underlying OI. In this context, the classification of OI has been revised several times and different types are used. The Sillence classification, based on clinical and radiological characteristics, is currently used as a grading of clinical severity. Based on the metabolic pathway, the functional classification allows identifying regulatory elements and targeting specific therapeutic approaches. Genetic classification has the advantage of identifying the inheritance pattern, an essential element for genetic counseling and prophylaxis. Although genotype-phenotype correlations may sometimes be challenging, genetic diagnosis allows a personalized management strategy, accurate family planning, and pregnancy management decisions including options for mode of delivery, or early antenatal OI treatment. Future research on molecular pathways and pathogenic variants involved could lead to the development of genotype-based therapeutic approaches. This narrative review summarizes our current understanding of genes, molecular mechanisms involved in OI, classifications, and their utility in prophylaxis.
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Affiliation(s)
- Monica-Cristina Panzaru
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi 700115, Romania
| | - Andreea Florea
- Department of Medical Genetics - Medical Genetics resident, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi 700115, Romania
| | - Lavinia Caba
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi 700115, Romania
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi 700115, Romania
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Syx D, Ishikawa Y, Gebauer J, Boudko SP, Guillemyn B, Van Damme T, D’hondt S, Symoens S, Nampoothiri S, Gould DB, Baumann U, Bächinger HP, Malfait F. Aberrant binding of mutant HSP47 affects posttranslational modification of type I collagen and leads to osteogenesis imperfecta. PLoS Genet 2021; 17:e1009339. [PMID: 33524049 PMCID: PMC7877763 DOI: 10.1371/journal.pgen.1009339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/11/2021] [Accepted: 01/05/2021] [Indexed: 12/21/2022] Open
Abstract
Heat shock protein 47 (HSP47), encoded by the SERPINH1 gene, is a molecular chaperone essential for correct folding of collagens. We report a homozygous p.(R222S) substitution in HSP47 in a child with severe osteogenesis imperfecta leading to early demise. p.R222 is a highly conserved residue located within the collagen interacting surface of HSP47. Binding assays show a significantly reduced affinity of HSP47-R222S for type I collagen. This altered interaction leads to posttranslational overmodification of type I procollagen produced by dermal fibroblasts, with increased glycosylation and/or hydroxylation of lysine and proline residues as shown by mass spectrometry. Since we also observed a normal intracellular folding and secretion rate of type I procollagen, this overmodification cannot be explained by prolonged exposure of the procollagen molecules to the modifying hydroxyl- and glycosyltransferases, as is commonly observed in other types of OI. We found significant upregulation of several molecular chaperones and enzymes involved in procollagen modification and folding on Western blot and RT-qPCR. In addition, we showed that an imbalance in binding of HSP47-R222S to unfolded type I collagen chains in a gelatin sepharose pulldown assay results in increased binding of other chaperones and modifying enzymes. The elevated expression and binding of this molecular ensemble to type I procollagen suggests a compensatory mechanism for the aberrant binding of HSP47-R222S, eventually leading to overmodification of type I procollagen chains. Together, these results illustrate the importance of HSP47 for proper posttranslational modification and provide insights into the molecular pathomechanisms of the p.(R222S) alteration in HSP47, which leads to a severe OI phenotype. Heat shock protein 47 (HSP47) is essential for correct collagen folding. We report a homozygous p.(R222S) substitution in HSP47 in a child with severe osteogenesis imperfecta. The highly conserved p.R222 residue is located within the collagen interacting surface and HSP47-R222S shows a significantly reduced affinity for type I collagen. This altered interaction leads to posttranslational overmodification of type I procollagen. In contrast to other types of OI, this overmodification is not caused by prolonged exposure of procollagen to modifying enzymes, since the intracellular folding rate of type I procollagen appears to be normal. We show significant upregulation of several molecular chaperones and collagen-modifying enzymes and increased binding of several of these molecules to unfolded type I collagen chains upon abnormal HSP47-R222S binding. This suggests a compensatory mechanism for aberrant HSP47-R222S binding, eventually leading to overmodification of type I procollagen chains, and underscores the importance of HSP47 for proper posttranslational modification.
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Affiliation(s)
- Delfien Syx
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Yoshihiro Ishikawa
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States of America
- Department of Ophthalmology, UCSF School of Medicine, San Francisco, California, United States of America
| | - Jan Gebauer
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Sergei P. Boudko
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Brecht Guillemyn
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tim Van Damme
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sanne D’hondt
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sofie Symoens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sheela Nampoothiri
- Amrita Institute of Medical Sciences and Research Center, Cochin, Kerala, India
| | - Douglas B. Gould
- Department of Ophthalmology, UCSF School of Medicine, San Francisco, California, United States of America
- Department of Anatomy, Institute for Human Genetics, UCSF School of Medicine, San Francisco, California, United States of America
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Hans Peter Bächinger
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- * E-mail:
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Li M, Zhang A, Li J, Zhou J, Zheng Y, Zhang C, Xia D, Mao H, Zhao J. Osteoblast/fibroblast coculture derived bioactive ECM with unique matrisome profile facilitates bone regeneration. Bioact Mater 2020; 5:938-948. [PMID: 32637756 PMCID: PMC7330453 DOI: 10.1016/j.bioactmat.2020.06.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/15/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
Extracellular matrix (ECM) with mimetic tissue niches was attractive to facilitate tissue regeneration in situ via recruitment of endogenous cells and stimulation of self-healing process. However, how to engineer the complicate tissue specific ECM with unique matrisome in vitro was a challenge of ECM-based biomaterials in tissue engineering and regenerative medicine. Here, we introduced coculture system to engineer bone mimetic ECM niche guided by cell-cell communication. In the cocultures, fibroblasts promoted osteogenic differentiation of osteoblasts via extracellular vesicles. The generated ECM (MN-ECM) displayed a unique appearance of morphology and biological components. The advantages of MN-ECM were demonstrated with promotion of multiple cellular behaviors (proliferation, adhesion and osteogenic mineralization) in vitro and bone regeneration in vivo. Moreover, proteomic analysis was used to clarify the molecular mechanism of MN-ECM, which revealed a specific matrisome signature. The present study provides a novel strategy to generate ECM with tissue mimetic niches via cell-cell communication in a coculture system, which forwards the development of tissue-bioactive ECM engineering along with deepening the understanding of ECM niches regulated by cells for bone tissue engineering.
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Affiliation(s)
- Mei Li
- Zhejiang Key Laboratory of Pathophysiology, Medical School in Ningbo University, Ningbo, Zhejiang, PR China
- Ningbo Institute of Medical Sciences, Ningbo, Zhejiang, PR China
| | - Anqi Zhang
- Zhejiang Key Laboratory of Pathophysiology, Medical School in Ningbo University, Ningbo, Zhejiang, PR China
| | - Jiajing Li
- Zhejiang Key Laboratory of Pathophysiology, Medical School in Ningbo University, Ningbo, Zhejiang, PR China
| | - Jing Zhou
- Zhejiang Key Laboratory of Pathophysiology, Medical School in Ningbo University, Ningbo, Zhejiang, PR China
| | - Yanan Zheng
- Zhejiang Key Laboratory of Pathophysiology, Medical School in Ningbo University, Ningbo, Zhejiang, PR China
| | - Chi Zhang
- Orthopedic Department, Ningbo First Hospital, Ningbo, Zhejiang, PR China
| | - Dongdong Xia
- Orthopedic Department, Ningbo First Hospital, Ningbo, Zhejiang, PR China
| | - Haijiao Mao
- Department of Orthopaedic Surgery, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang, PR China
| | - Jiyuan Zhao
- Zhejiang Key Laboratory of Pathophysiology, Medical School in Ningbo University, Ningbo, Zhejiang, PR China
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