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

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.

CLEC16A—An Emerging Master Regulator of Autoimmunity and Neurodegeneration

“…However, when faced with metabolic stressors associated with diabetes, such as high levels of glucose and fatty acids, the CLEC16A-RNF41-USP8 complex becomes destabilized and can lead to the death of β-cells. Another recent study additionally confirmed the above interaction of CLEC16A with NRDP1 also known as RNF41 [123]. CLEC16A-mediated mitophagy modulation is depicted in Figure 5.…”

“…A recent study reported the first bi-allelic loss-of-function (LoF) CLEC16A truncating variants in siblings from two unrelated families with a severe neurodevelopmental disorder, including microcephaly, brain atrophy, corpus callosum dysgenesis, growth retardation, and hypotonia with severe developmental delay [123]. Using zebrafish as an in vivo model, the study shows that the loss of CLEC16A disrupts both autophagy and mitophagy, already during brain development.…”

In Search of a Target Gene for a Desirable Phenotype in Aquaculture: Genome Editing of Cyprinidae and Salmonidae Species

“…Genome editing has been used to model human tumors such as liver cancer [70], paraganglioma [71], skin melanoma [72], and epithelioid sarcoma [73]. Among neurologic diseases, amyotrophic lateral sclerosis [74], epilepsy [75][76][77][78][79] [105,106], inner ear [107][108][109][110][111], vestibular apparatus [111], otoliths [112], brain [89, [113][114][115][116][117], neural tissue [118][119][120][121][122][123][124][125][126][127] and nervous system [128][129][130], heart [131][132][133][134][135][136][137][138][139], cardiomyocytes [140][141]…”

“…Much of the work has focused on the role of specific genes in organ formation and function, including the lens [ 99 ], retina [ 100 , 101 , 102 ], optic neurons [ 103 , 104 ], ocular vessels [ 105 , 106 ], inner ear [ 107 , 108 , 109 , 110 , 111 ], vestibular apparatus [ 111 ], otoliths [ 112 ], brain [ 89 , 113 , 114 , 115 , 116 , 117 ], neural tissue [ 118 , 119 , 120 , 121 , 122 , 123 , 124 , 125 , 126 , 127 ] and nervous system [ 128 , 129 , 130 ], heart [ 131 , 132 , 133 , 134 , 135 , 136 , 137 , 138 , 139 ], cardiomyocytes [ 140 , 141 , 142 , 143 ], including cardiovascular rate control [ 144 , 145 ], blood vessels [ 146 , 147 ,…”