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Tian X, Zhang X, Zhang Q, Chen X, Zhou B, Ma P, zheng L, Hao S, Ling J, Zhang C, Hui L. Immune skeletal dysplasia with neurodevelopmental abnormalities caused by a novel variant of EXTL3 gene in a Chinese family. Mol Genet Genomic Med 2024; 12:e2308. [PMID: 38010033 PMCID: PMC10767689 DOI: 10.1002/mgg3.2308] [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: 04/13/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Immune skeletal dysplasia with neurodevelopmental abnormalities (ISDNA) is an extremely rare, autosomal recessive genetic disorder characterized by various skeletal abnormalities, neurodevelopmental deficits, and abnormal immune system function. ISDNA is caused by variation in the exostosin-like 3 (EXTL3) gene, located on chromosome 8p21.2, whose primary function is the biosynthesis of heparan sulfate (HS) skeleton structure. Only a few variations in the EXTL3 gene have been discovered so far. In these years of development, many pathogenic variants in genetic diseases with genetic and phenotypic heterogeneity have been investigated using whole-exome sequencing (WES) technology. METHODS In this research, a novel EXTL3 variant was first detected in a patient using WES, which was validated from Sanger sequencing in this family. Family history and clinical information were then collected through comprehensive medical examinations and genetic counseling. In silico prediction was then utilized to confirm the pathogenicity of the variant. RESULTS A novel homozygous variant, NM_001440: c.2015G>A (p.Arg672Gln) in the EXTL3 gene, was identified using WES, which has never been reported before. Sanger sequencing was performed to confirm that the variant segregated with the disease within the family. CONCLUSION This research identified a novel pathogenic variant in the EXTL3 gene responsible for ISDNA in a Chinese family. It showed the potential diagnostic role of WES in ISDNA, expanded the EXTL3 gene variation spectrum, and demonstrated that the diagnosis of ISDNA using WES is feasible and effective. More comprehensive genetic counseling and precise prenatal diagnosis for the next pregnancy can also be provided to families with genetic disorders.
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Affiliation(s)
- Xinyuan Tian
- Center for Medical GeneticsGansu Provincial Maternity and Child Care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
- School of Public HealthGansu University of Chinese MedicineLanzhouChina
| | - Xiaoni Zhang
- Center for Early Childhood DevelopmentGansu Provincial Maternity and Child‐Care HospitalLanzhouChina
| | - Qinghua Zhang
- Center for Medical GeneticsGansu Provincial Maternity and Child Care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Xue Chen
- Center for Medical GeneticsGansu Provincial Maternity and Child Care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Bingbo Zhou
- Center for Medical GeneticsGansu Provincial Maternity and Child Care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Panpan Ma
- Center for Medical GeneticsGansu Provincial Maternity and Child Care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Lei zheng
- Center for Medical GeneticsGansu Provincial Maternity and Child Care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Shengju Hao
- Center for Medical GeneticsGansu Provincial Maternity and Child Care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Junhe Ling
- School of Public HealthGansu University of Chinese MedicineLanzhouChina
| | - Chuan Zhang
- Center for Medical GeneticsGansu Provincial Maternity and Child Care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Ling Hui
- Center for Medical GeneticsGansu Provincial Maternity and Child Care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
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Sammon D, Krueger A, Busse-Wicher M, Morgan RM, Haslam SM, Schumann B, Briggs DC, Hohenester E. Molecular mechanism of decision-making in glycosaminoglycan biosynthesis. Nat Commun 2023; 14:6425. [PMID: 37828045 PMCID: PMC10570366 DOI: 10.1038/s41467-023-42236-z] [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: 04/26/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Two major glycosaminoglycan types, heparan sulfate (HS) and chondroitin sulfate (CS), control many aspects of development and physiology in a type-specific manner. HS and CS are attached to core proteins via a common linker tetrasaccharide, but differ in their polymer backbones. How core proteins are specifically modified with HS or CS has been an enduring mystery. By reconstituting glycosaminoglycan biosynthesis in vitro, we establish that the CS-initiating N-acetylgalactosaminyltransferase CSGALNACT2 modifies all glycopeptide substrates equally, whereas the HS-initiating N-acetylglucosaminyltransferase EXTL3 is selective. Structure-function analysis reveals that acidic residues in the glycopeptide substrate and a basic exosite in EXTL3 are critical for specifying HS biosynthesis. Linker phosphorylation by the xylose kinase FAM20B accelerates linker synthesis and initiation of both HS and CS, but has no effect on the subsequent polymerisation of the backbone. Our results demonstrate that modification with CS occurs by default and must be overridden by EXTL3 to produce HS.
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Affiliation(s)
- Douglas Sammon
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Anja Krueger
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Marta Busse-Wicher
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Abzena, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Rhodri Marc Morgan
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- ZoBio, 2333 CH, Leiden, Netherlands
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Benjamin Schumann
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Chemical Glycobiology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - David C Briggs
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
| | - Erhard Hohenester
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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Wilson LFL, Dendooven T, Hardwick SW, Echevarría-Poza A, Tryfona T, Krogh KBRM, Chirgadze DY, Luisi BF, Logan DT, Mani K, Dupree P. The structure of EXTL3 helps to explain the different roles of bi-domain exostosins in heparan sulfate synthesis. Nat Commun 2022; 13:3314. [PMID: 35676258 PMCID: PMC9178029 DOI: 10.1038/s41467-022-31048-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Heparan sulfate is a highly modified O-linked glycan that performs diverse physiological roles in animal tissues. Though quickly modified, it is initially synthesised as a polysaccharide of alternating β-D-glucuronosyl and N-acetyl-α-D-glucosaminyl residues by exostosins. These enzymes generally possess two glycosyltransferase domains (GT47 and GT64)-each thought to add one type of monosaccharide unit to the backbone. Although previous structures of murine exostosin-like 2 (EXTL2) provide insight into the GT64 domain, the rest of the bi-domain architecture is yet to be characterised; hence, how the two domains co-operate is unknown. Here, we report the structure of human exostosin-like 3 (EXTL3) in apo and UDP-bound forms. We explain the ineffectiveness of EXTL3's GT47 domain to transfer β-D-glucuronosyl units, and we observe that, in general, the bi-domain architecture would preclude a processive mechanism of backbone extension. We therefore propose that heparan sulfate backbone polymerisation occurs by a simple dissociative mechanism.
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Affiliation(s)
- L F L Wilson
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
| | - T Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - S W Hardwick
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - A Echevarría-Poza
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - T Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - K B R M Krogh
- Department of Protein Biochemistry and Stability, Novozymes A/S, Krogshøjvej 36, 2880, Bagsværd, Denmark
| | - D Y Chirgadze
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - B F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - D T Logan
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00, Lund, Sweden
| | - K Mani
- Department of Experimental Medical Science, Division of Neuroscience, Glycobiology Group, Lund University, SE-221 00, Lund, Sweden.
| | - P Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
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Bajaj S, Satoskar P, Nair A, Sheth F, Sheth J, Sheth H. An ultra-rare case of immunoskeletal dysplasia with neurodevelopmental abnormalities in an Indian patient with homozygous c.953C > T variant in EXTL3 gene: a case report. BMC Pediatr 2022; 22:78. [PMID: 35114981 PMCID: PMC8812182 DOI: 10.1186/s12887-022-03143-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 01/26/2022] [Indexed: 12/19/2022] Open
Abstract
Background Immunoskeletal dysplasia with neurodevelopmental abnormalities (ISDNA) is an ultra-rare genetic condition that belongs to the group of spondyloepimetaphyseal dysplasias. It is caused due to presence of biallelic variants in the EXTL3 gene. The encoded exostosin like glycosyltransferase 3 (EXTL3) protein plays a key role in heparan sulfate synthesis. The skeletal and nervous systems are prominently affected in ISDNA with variability in immunological manifestations. Here, we report the 15th case of ISDNA (third patient of an Indian ancestry) in the world, along with a review of literature. Case presentation A 15-month-old female child with clinical indications of global developmental delay, short stature, coarse facial features, and hypotonia was referred to our clinic. Spondyloepimetaphyseal dysplasias associated with extra-skeletal manifestations was suspected based on clinic-radiological correlation. Whole exome sequencing analysis revealed the presence of a homozygous known pathogenic variant c.953C > T (p. Pro318Leu) in exon 3 of the EXTL3 gene, thereby confirming diagnosis of ISDNA. Conclusion We present an ultra-rare case of ISDNA- third patient of Indian ancestry and only the 15th reported case in the literature. On review of all cases in the literature, we find that the affected individuals show abnormalities primarily in three systems namely- skeletal, nervous and immune system. Notably, patients harbouring the same variant in EXTL3 gene show phenotypic variability especially with respect to presence or absence of immunological manifestations, suggesting a role of unknown modifiers. Hence, it is currently not possible to correlate the variant position in the EXTL3 gene with disease severity.
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Affiliation(s)
- Shruti Bajaj
- The Purple Gene Clinic, Simplex Khushaangan, SV Road, Malad West, Mumbai, 400064, Maharashtra, India
| | - Purnima Satoskar
- Department of Obstetrics and Gynaecology, Nowrosjee Wadia Maternity Hospital and Seth G. S. Medical College, Acharya Donde Marg, Parel, Mumbai, 400012, India
| | - Aadhira Nair
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India
| | - Frenny Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India
| | - Harsh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India.
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Yamada S. Specific functions of Exostosin-like 3 ( EXTL3) gene products. Cell Mol Biol Lett 2020; 25:39. [PMID: 32843889 PMCID: PMC7441721 DOI: 10.1186/s11658-020-00231-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022] Open
Abstract
Exostosin-like 3 (EXTL3) encodes the glycosyltransferases responsible for the biosynthesis of the backbone structure of heparan sulfate (HS), a sulfated polysaccharide that is ubiquitously distributed on the animal cell surface and in the extracellular matrix. A lack of EXTL3 reduces HS levels and causes embryonic lethality, indicating its indispensable role in the biosynthesis of HS. EXTL3 has also been identified as a receptor molecule for regenerating islet-derived (REG) protein ligands, which have been shown to stimulate islet β-cell growth. REG proteins also play roles in keratinocyte proliferation and/or differentiation, tissue regeneration and immune defenses in the gut as well as neurite outgrowth in the central nervous system. Compared with the established function of EXTL3 as a glycosyltransferase in HS biosynthesis, the REG-receptor function of EXTL3 is not conclusive. Genetic diseases caused by biallelic mutations in the EXTL3 gene were recently reported to result in a neuro-immuno-skeletal dysplasia syndrome. EXTL3 is a key molecule for the biosynthesis of HS and may be involved in the signal transduction of REG proteins.
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Affiliation(s)
- Shuhei Yamada
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, 468-8503 Japan
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Discovery of three novel sesquiterpene synthases from Streptomyces chartreusis NRRL 3882 and crystal structure of an α-eudesmol synthase. J Biotechnol 2019; 297:71-77. [PMID: 30928538 DOI: 10.1016/j.jbiotec.2019.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/11/2019] [Accepted: 03/14/2019] [Indexed: 12/11/2022]
Abstract
With more than 50,000 members, terpenoids are one of the most important classes of natural products and show an enormous diversity. Due to their unique odors and specific bioactivities they already find wide application in the flavor, fragrance and pharma industries. Since most terpenoids can only be obtained by natural product extraction, the discovery of biosynthetic genes for the generation of terpene diversity becomes increasingly important. This study describes the discovery of three novel sesquiterpene synthases from Streptomyces chartreusis with preference for the formation of germacradiene-11-ol, α-eudesmol and α-amorphene respectively. The α-eudesmol synthase showed formation of 10-epi-δ-eudesmol and elemol as side products. Eudesmol-isomers are known to have repellent activity, which makes this enzyme a potential catalyst for products for the prevention of mosquito-related disease. The determination of the structure of the apo-enzyme of α-eudesmol synthase from S. chartreusis provides the first structural insights into an eudesmol-forming enzyme.
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