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10.1172/JCI196452
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Burns, K. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Zaman, M. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Young, D. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Hua, M. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Gao, Y. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Or, Y. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Nobakht, F. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Webb, B. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Jurgens, J. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Ramond, F. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Wei, X. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Robson, C. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Pagnamenta, A. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Megaly, M. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Tafech, B. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
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1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Shutt, T. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Au, P. in: PubMed | Google Scholar
1Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
2Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
3Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
4Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
5Department of Neurology, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, United States of America
6Department of Genetics, Saint-Étienne University Hospital, Saint-Étienne, France
7Diagnostic Imaging, Alberta Children’s Hospital, Calgary, Canada
8Department of Radiology, Boston Children’s Hospital and Harvard University, Boston, United States of America
9Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
10Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Find articles by Yang, G. in: PubMed | Google Scholar
Published October 6, 2026 - More info
During organogenesis, stem cells undergo cellular and metabolic remodelling, facilitated by autophagy-mediated turnover of organelles. Autophagy impairment has been linked to human diseases, including neurodevelopmental disorders associated with disrupted neural stem/precursor cell (NPC) homeostasis, but the underlying mechanisms and pathogenic processes governing these connections remain poorly understood. Here, we report three de novo variants of uncertain significance (p.Gly223Asp, p.Gly889Glu, p.Met978Val) in the deubiquitinase USP15 in human probands with diverse clinical features, including a spectrum of brain malformations and metabolic phenotypes. Proband variants differentially altered USP15 activity and nucleocytoplasmic localization. USP15 showed dynamic localization in NPCs of embryonic mouse cerebral cortex. Using a knock-in mouse model carrying the p.Met978Val variant, we showed that aberrant cytoplasmic accumulation of USP15, but not its loss-of-function, impaired NPC self-renewal and differentiation, leading to reduced neuronal output and enlarged lateral ventricles. Mechanistically, USP15 deubiquitinated autophagy regulator ATG16L1, impeded its normal turnover, and impaired autophagy. Concurrently, lipid droplet mobilization and mitochondrial dynamics were attenuated. Reestablishing the ubiquitination-deubiquitination balance restored autophagy activity and normal neurogenesis. Our findings suggest that nucleocytoplasmic shuttling of USP15 creates a switch-like autophagy signal controlling NPC homeostasis, and its disruption may contribute to the pathogenesis of complex neurodevelopmental conditions.