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Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly

Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly
Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly

Background: Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been implicated in human diseases known collectively as “coatopathies”. Methods: Whole exome or genome sequencing of two families with a neuro-developmental syndrome, variable microcephaly and cataracts revealed biallelic variants in COPB1, which encodes the beta-subunit of COPI (β-COP). To investigate Family 1’s splice donor site variant, we undertook patient blood RNA studies and CRISPR/Cas9 modelling of this variant in a homologous region of the Xenopus tropicalis genome. To investigate Family 2’s missense variant, we studied cellular phenotypes of human retinal epithelium and embryonic kidney cell lines transfected with a COPB1 expression vector into which we had introduced Family 2’s mutation. Results: We present a new recessive coatopathy typified by severe developmental delay and cataracts and variable microcephaly. A homozygous splice donor site variant in Family 1 results in two aberrant transcripts, one of which causes skipping of exon 8 in COPB1 pre-mRNA, and a 36 amino acid in-frame deletion, resulting in the loss of a motif at a small interaction interface between β-COP and β’-COP. Xenopus tropicalis animals with a homologous mutation, introduced by CRISPR/Cas9 genome editing, recapitulate features of the human syndrome including microcephaly and cataracts. In vitro modelling of the COPB1 c.1651T>G p.Phe551Val variant in Family 2 identifies defective Golgi to ER recycling of this mutant β-COP, with the mutant protein being retarded in the Golgi. Conclusions: This adds to the growing body of evidence that COPI subunits are essential in brain development and human health and underlines the utility of exome and genome sequencing coupled with Xenopus tropicalis CRISPR/Cas modelling for the identification and characterisation of novel rare disease genes.

COPB1, COPI, Cataract, Coatomer, Intellectual disability, Microcephaly, Xenopus model, β-COP
1756-994X
34
Macken, William
7ec76437-8d75-4be4-a73b-aa7735f942d1
Godwin, Annie
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Wheway, Gabrielle
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Stals, Karen
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Nazlamova, Liliya
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Ellard, Sian
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Alfares, Ahmed
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Aloraini, Taghrid
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AlSubaie, Lamia
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Alfadhel, Majid
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Alajaji, Sulaiman
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Wai, Htoo
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Self, James
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Douglas, Andrew
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Kao, Alexander
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Guille, Matthew
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Baralle, Diana
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Macken, William
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Godwin, Annie
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Wheway, Gabrielle
2e547e5d-b921-4243-a071-2208fd4cc090
Stals, Karen
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Nazlamova, Liliya
0cc21013-aeeb-4eef-af56-31f6fa0766fd
Ellard, Sian
6c9b0ede-8980-4602-b063-444b165baa09
Alfares, Ahmed
a0182507-03f5-47e1-a1f6-eaae4cd74b88
Aloraini, Taghrid
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AlSubaie, Lamia
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Alfadhel, Majid
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Alajaji, Sulaiman
2eef03e9-e946-4ac3-8fdc-bcabe5d29483
Wai, Htoo
4428517b-33b3-42cb-9818-ca64763ab7bc
Self, James
0f6efc58-ae24-4667-b8d6-6fafa849e389
Douglas, Andrew
2c789ec4-a222-43bc-a040-522ca64fea42
Kao, Alexander
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Guille, Matthew
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Baralle, Diana
faac16e5-7928-4801-9811-8b3a9ea4bb91

Macken, William, Godwin, Annie, Wheway, Gabrielle, Stals, Karen, Nazlamova, Liliya, Ellard, Sian, Alfares, Ahmed, Aloraini, Taghrid, AlSubaie, Lamia, Alfadhel, Majid, Alajaji, Sulaiman, Wai, Htoo, Self, James, Douglas, Andrew, Kao, Alexander, Guille, Matthew and Baralle, Diana (2021) Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly. Genome Medicine, 13 (1), 34, [34]. (doi:10.1186/s13073-021-00850-w).

Record type: Article

Abstract

Background: Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been implicated in human diseases known collectively as “coatopathies”. Methods: Whole exome or genome sequencing of two families with a neuro-developmental syndrome, variable microcephaly and cataracts revealed biallelic variants in COPB1, which encodes the beta-subunit of COPI (β-COP). To investigate Family 1’s splice donor site variant, we undertook patient blood RNA studies and CRISPR/Cas9 modelling of this variant in a homologous region of the Xenopus tropicalis genome. To investigate Family 2’s missense variant, we studied cellular phenotypes of human retinal epithelium and embryonic kidney cell lines transfected with a COPB1 expression vector into which we had introduced Family 2’s mutation. Results: We present a new recessive coatopathy typified by severe developmental delay and cataracts and variable microcephaly. A homozygous splice donor site variant in Family 1 results in two aberrant transcripts, one of which causes skipping of exon 8 in COPB1 pre-mRNA, and a 36 amino acid in-frame deletion, resulting in the loss of a motif at a small interaction interface between β-COP and β’-COP. Xenopus tropicalis animals with a homologous mutation, introduced by CRISPR/Cas9 genome editing, recapitulate features of the human syndrome including microcephaly and cataracts. In vitro modelling of the COPB1 c.1651T>G p.Phe551Val variant in Family 2 identifies defective Golgi to ER recycling of this mutant β-COP, with the mutant protein being retarded in the Golgi. Conclusions: This adds to the growing body of evidence that COPI subunits are essential in brain development and human health and underlines the utility of exome and genome sequencing coupled with Xenopus tropicalis CRISPR/Cas modelling for the identification and characterisation of novel rare disease genes.

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Accepted/In Press date: 11 February 2021
e-pub ahead of print date: 25 February 2021
Published date: 25 February 2021
Additional Information: Funding Information: The authors greatly appreciate the participation of the patients and their families in this study. Identification of one of the participating families was made possible by the GeneMatcher portal. We thank the Zeiss Global Centre based at the University of Portsmouth for providing the X-ray MicroCT imaging and data processing facilities. We are grateful to Dr. Colin Sharpe, University of Portsmouth, for his expert feedback on the manuscript. Part of this research was funded by the National Institute for Health Research (NIHR). Funding Information: DB is generously supported by a National Institute of Health Research (NIHR) Research Professorship RP-2016-07-011. GW is supported by a Wellcome Trust Seed Award in Science 204378/Z/16/Z. We acknowledge support from the NIHR UK Rare Genetic Disease Research Consortium. The European Xenopus Reference Centre is supported by the Wellcome Trust (101480Z) and BBSRC (BB/K019988/1). Publisher Copyright: © 2021, The Author(s).
Keywords: COPB1, COPI, Cataract, Coatomer, Intellectual disability, Microcephaly, Xenopus model, β-COP

Identifiers

Local EPrints ID: 447061
URI: http://eprints.soton.ac.uk/id/eprint/447061
ISSN: 1756-994X
PURE UUID: bdf12ce4-6a15-45f9-bdea-45ecb54368b6
ORCID for Gabrielle Wheway: ORCID iD orcid.org/0000-0002-0494-0783
ORCID for Htoo Wai: ORCID iD orcid.org/0000-0002-3560-6980
ORCID for James Self: ORCID iD orcid.org/0000-0002-1030-9963
ORCID for Andrew Douglas: ORCID iD orcid.org/0000-0001-5154-6714
ORCID for Diana Baralle: ORCID iD orcid.org/0000-0003-3217-4833

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Date deposited: 02 Mar 2021 17:32
Last modified: 17 Mar 2024 03:53

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Contributors

Author: William Macken
Author: Annie Godwin
Author: Karen Stals
Author: Liliya Nazlamova
Author: Sian Ellard
Author: Ahmed Alfares
Author: Taghrid Aloraini
Author: Lamia AlSubaie
Author: Majid Alfadhel
Author: Sulaiman Alajaji
Author: Htoo Wai ORCID iD
Author: James Self ORCID iD
Author: Andrew Douglas ORCID iD
Author: Alexander Kao
Author: Matthew Guille
Author: Diana Baralle ORCID iD

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