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ResearchIn-Press PreviewCell biologyDevelopmentNeuroscience Open Access | 10.1172/JCI196452

Nucleocytoplasmic shuttling of USP15 promotes pathological autophagy that disrupts neural stem cell homeostasis and neurodevelopment

Kaylan M.L. Burns,1 Mashiat Zaman,1 Daniel Young,2 Michelle Hua,1 Yu-Yun Gao,1 Yvonne Yan Yan Or,3 Farzaneh Nobakht,1 Bryn D. Webb,4 Julie A. Jurgens,5 Francis Ramond,6 Xing-Chang Wei,7 Caroline D. Robson,8 Alistair T. Pagnamenta,9 Marvel Megaly,3 Belal Tafech,3 Antoine Dufour,2 Timothy E. Shutt,1 Ping Yee Billie Au,10 and Guang Yang3

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

Find articles by Dufour, 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 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

J Clin Invest. https://doi.org/10.1172/JCI196452.
Copyright © 2026, Burns et al. This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Published October 6, 2026 - Version history
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Abstract

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.

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