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Brain. 2020 Jan 1;143(1):112-130. doi: 10.1093/brain/awz374.

Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability.

Author information

1
Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.
2
Department of Paediatrics, University of Melbourne, Melbourne, Australia.
3
Center for Applied Genomics (CAG) at the Children's Hospital of Philadelphia (CHOP), Philadelphia, USA.
4
Department of Biology, Concordia University, Montreal, Quebec, Canada.
5
Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.
6
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA.
7
Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA.
8
Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, 34303, Turkey.
9
TY Nelson Department of Neurology and Neurosurgery, Children's Hospital at Westmead, Sydney, Australia.
10
Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.
11
Medical Genomics Department, Royal Prince Alfred Hospital, Sydney, Australia.
12
Department of Pediatrics, Naval Medical Center San Diego, San Diego, California, USA.
13
Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA.
14
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
15
Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
16
Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA.
17
Texas Children's Hospital, Houston, Texas, 77030, USA.
18
Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.
19
Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia.
20
Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia.

Abstract

The conserved transport protein particle (TRAPP) complexes regulate key trafficking events and are required for autophagy. TRAPPC4, like its yeast Trs23 orthologue, is a core component of the TRAPP complexes and one of the essential subunits for guanine nucleotide exchange factor activity for Rab1 GTPase. Pathogenic variants in specific TRAPP subunits are associated with neurological disorders. We undertook exome sequencing in three unrelated families of Caucasian, Turkish and French-Canadian ethnicities with seven affected children that showed features of early-onset seizures, developmental delay, microcephaly, sensorineural deafness, spastic quadriparesis and progressive cortical and cerebellar atrophy in an effort to determine the genetic aetiology underlying neurodevelopmental disorders. All seven affected subjects shared the same identical rare, homozygous, potentially pathogenic variant in a non-canonical, well-conserved splice site within TRAPPC4 (hg19:chr11:g.118890966A>G; TRAPPC4: NM_016146.5; c.454+3A>G). Single nucleotide polymorphism array analysis revealed there was no haplotype shared between the tested Turkish and Caucasian families suggestive of a variant hotspot region rather than a founder effect. In silico analysis predicted the variant to cause aberrant splicing. Consistent with this, experimental evidence showed both a reduction in full-length transcript levels and an increase in levels of a shorter transcript missing exon 3, suggestive of an incompletely penetrant splice defect. TRAPPC4 protein levels were significantly reduced whilst levels of other TRAPP complex subunits remained unaffected. Native polyacrylamide gel electrophoresis and size exclusion chromatography demonstrated a defect in TRAPP complex assembly and/or stability. Intracellular trafficking through the Golgi using the marker protein VSVG-GFP-ts045 demonstrated significantly delayed entry into and exit from the Golgi in fibroblasts derived from one of the affected subjects. Lentiviral expression of wild-type TRAPPC4 in these fibroblasts restored trafficking, suggesting that the trafficking defect was due to reduced TRAPPC4 levels. Consistent with the recent association of the TRAPP complex with autophagy, we found that the fibroblasts had a basal autophagy defect and a delay in autophagic flux, possibly due to unsealed autophagosomes. These results were validated using a yeast trs23 temperature sensitive variant that exhibits constitutive and stress-induced autophagic defects at permissive temperature and a secretory defect at restrictive temperature. In summary we provide strong evidence for pathogenicity of this variant in a member of the core TRAPP subunit, TRAPPC4 that associates with vesicular trafficking and autophagy defects. This is the first report of a TRAPPC4 variant, and our findings add to the growing number of TRAPP-associated neurological disorders.

KEYWORDS:

autophagy; intellectual disability; molecular genetics; vesicular transport; whole-exome sequencing

PMID:
31794024
PMCID:
PMC6935753
[Available on 2021-01-01]
DOI:
10.1093/brain/awz374

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