Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment

Abstract

Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or “primed” by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.

Polioencephalopathy in Eurasier dogs

“…The ATG4D variations result in disruption of neuronal homeostasis, particularly in the axons and Purkinje cells, structures known to be dependent on basal autophagy. 38 , 39 , 40 , 41 An ATG4D :p.Ala430Thr variant previously has been associated with a recessive vacuolar storage disease in the Lagotto Romagnolo. 40 Although in these 3 Eurasier dogs clinical signs also support abnormal function of the cerebellum, some clear disparities exist both clinically and in MRI studies between the Lagotto Romagnolo and our dogs with a variant in the ATG4D gene.…”

Inhibition of miR-542-3p augments autophagy to promote diabetic corneal wound healing

“…An increasing number of studies have shown that dysfunctional autophagy leads to neurological dysfunction and neurodegenerative pathologies [ 32 – 34 ]. Aberrant expression of Atg4B and Atg5 has also been found in diabetic corneal nerves, suggesting that dysregulated autophagy is also involved in diabetic corneal neuropathy [ 21 , 22 ].…”

“…ATG4D is the main delipidating enzyme of mATG8 and facilitates autophagosome formation, removing abnormal protein accumulation to protect neurons [ 40 – 42 ]. Deficiency or mutation of ATG4D causes cerebellar neurodegeneration and neurodevelopmental disorders [ 34 , 41 ]. However, there are no studies on ATG4D in diabetic corneal neuropathy.…”

A nerve-wracking buzz: lessons from Drosophila models of peripheral neuropathy and axon degeneration

“…The number of human genomics studies who complete their first in vivo validations in Drosophila is growing. Additionally, a network of laboratories has united to use model organisms as rare disease profiling platforms, with Drosophila as one of the leaders in this movement ( Gahl et al, 2015 ; Huang et al, 2022 ; Morimoto et al, 2023 ; Srivastava et al, 2023 ). For more established models of diseases such as ALS, flies will continue to provide a platform for unbiased, in vivo screening for enhancers and suppressors of nerve degeneration and cell loss.…”