CLEC16A interacts with retromer and TRIM27, and its loss impairs endosomal trafficking and neurodevelopment

Daphne J. Smits*, Jordy Dekker*, Rachel Schot, Brahim Tabarki, Amal Alhashem, Jeroen A.A. Demmers, Dick H.W. Dekkers, Antonio Romito, Peter J. van der Spek, Tjakko J. van Ham, Aida M. Bertoli-Avella, Grazia M.S. Mancini, Peter Verrijzer

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)
32 Downloads (Pure)

Abstract

CLEC16A is a membrane-associated C-type lectin protein that functions as a E3-ubiquitin ligase. CLEC16A regulates autophagy and mitophagy, and reportedly localizes to late endosomes. GWAS studies have associated CLEC16A SNPs to various auto-immune and neurological disorders, including multiple sclerosis and Parkinson disease. Studies in mouse models imply a role for CLEC16A in neurodegeneration. We identified bi-allelic CLEC16A truncating variants in siblings from unrelated families presenting with a severe neurodevelopmental disorder including microcephaly, brain atrophy, corpus callosum dysgenesis, and growth retardation. To understand the function of CLEC16A in neurodevelopment we used in vitro models and zebrafish embryos. We observed CLEC16A localization to early endosomes in HEK293T cells. Mass spectrometry of human CLEC16A showed interaction with endosomal retromer complex subunits and the endosomal ubiquitin ligase TRIM27. Expression of the human variant leading to C-terminal truncated CLEC16A, abolishes both its endosomal localization and interaction with TRIM27, suggesting a loss-of-function effect. CLEC16A knockdown increased TRIM27 adhesion to early endosomes and abnormal accumulation of endosomal F-actin, a sign of disrupted vesicle sorting. Mutagenesis of clec16a by CRISPR–Cas9 in zebrafish embryos resulted in accumulated acidic/phagolysosome compartments, in neurons and microglia, and dysregulated mitophagy. The autophagocytic phenotype was rescued by wild-type human CLEC16A but not the C-terminal truncated CLEC16A. Our results demonstrate that CLEC16A closely interacts with retromer components and regulates endosomal fate by fine-tuning levels of TRIM27 and polymerized F-actin on the endosome surface. Dysregulation of CLEC16A-mediated endosomal sorting is associated with neurodegeneration, but it also causes accumulation of autophagosomes and unhealthy mitochondria during brain development.

Original languageEnglish
Pages (from-to)379-397
Number of pages19
JournalHuman Genetics
Volume142
Issue number3
Early online date20 Dec 2022
DOIs
Publication statusPublished - Mar 2023

Bibliographical note

Funding Information:
GMSM and DJS are supported by ZonMW Top grant #9127045.

Funding Information:
We thank the families for participating in this study. This publication is, in part, a result of collaboration within the European Network on Brain Malformations funded by COST (European Cooperation in Science and Technology, Action CA16118). We thank prof. Vincenzo Bonifati, Erasmus MC Rotterdam, for sharing material for immunostainings, Dr. Marvin M. Van Luijn, Erasmus MC Rotterdam, for sharing plasmids and Dr. Stefania Marina, Erasmus MC Rotterdam, for sharing anti-Parkin antibody. We thank Dr. Marina Bakay, CHOP, Philadelphia, for critically reading the manuscript and prof. Hakon Hakonarson, CHOP, Philadelphia, for fruitful discussions.

Funding Information:
We thank the families for participating in this study. This publication is, in part, a result of collaboration within the European Network on Brain Malformations funded by COST (European Cooperation in Science and Technology, Action CA16118). We thank prof. Vincenzo Bonifati, Erasmus MC Rotterdam, for sharing material for immunostainings, Dr. Marvin M. Van Luijn, Erasmus MC Rotterdam, for sharing plasmids and Dr. Stefania Marina, Erasmus MC Rotterdam, for sharing anti-Parkin antibody. We thank Dr. Marina Bakay, CHOP, Philadelphia, for critically reading the manuscript and prof. Hakon Hakonarson, CHOP, Philadelphia, for fruitful discussions.

Publisher Copyright:
© 2022, The Author(s).

Fingerprint

Dive into the research topics of 'CLEC16A interacts with retromer and TRIM27, and its loss impairs endosomal trafficking and neurodevelopment'. Together they form a unique fingerprint.

Cite this