Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms
Abstract RNA splicing shapes neuronal identity and disease risk, yet current maps lack the developmental resolution and depth to resolve this complexity. Here, we integrate deep long-read RNA sequencing and proteomics in iPSC-derived cortical neurons to generate a high-resolution proteogenomic atlas of human neuron development. We identify 182,371 mRNA isoforms (over half previously unknown) and provide direct peptide evidence for the translation of hundreds of novel protein-coding sequences. Population genetics demonstrates that variants affecting novel exons and splice sites are under negative selection, underscoring the potential significance of these isoforms. During neuronal maturation, we observe that ASD risk genes undergo dynamic isoform switching, including microexon inclusion and intron retention, that remodel key protein domains and regulatory regions. Furthermore, we uncover widespread, long-range coordination between splicing and polyadenylation. Finally, our atlas enables variant reinterpretation in ASD, highlighting the value of an isoform-centric view for interpreting pathogenic variation in neurodevelopment.
Authors
- Elizabeth Radley (ORCID: https://orcid.org/0000-0002-8156-1381)
- Melanie Davie (ORCID: https://orcid.org/0000-0001-8183-8064)
- Ai Tian (ORCID: https://orcid.org/0009-0000-1849-0624)
- Chaoying Long
- Ellie Hogan
- Hyun O. Lee (ORCID: https://orcid.org/0000-0003-0102-4795)
- Howard D. Lipshitz (ORCID: https://orcid.org/0000-0002-7372-4419)
- Craig A. Smibert (ORCID: https://orcid.org/0000-0001-6375-8669)
- Julien Muffat (ORCID: https://orcid.org/0000-0003-1889-7023)
- Maria Fafouti
- Brett Trost (ORCID: https://orcid.org/0000-0003-4863-7273)
- John A. Calarco (ORCID: https://orcid.org/0000-0002-2197-7801)
- Shreejoy J. Tripathy (ORCID: https://orcid.org/0000-0002-1007-9061)
- Yun Li (ORCID: https://orcid.org/0000-0002-5849-5910)
- Nuo Xu (ORCID: https://orcid.org/0009-0001-3405-4846)
- Hua Luo (ORCID: https://orcid.org/0000-0002-4997-3845)
- Jimmy Li (ORCID: https://orcid.org/0009-0004-8585-9347)
- Maahil Arshad (ORCID: https://orcid.org/0009-0001-8979-3072)
- Katherine M. Rynard
- Fatima Naimi
Institutions
- Centre for Addiction and Mental Health (CA)
- University of Toronto (CA)
- Great Ormond Street Hospital (GB)
- Hospital for Sick Children (CA)
- SickKids Foundation (CA)
- Whitehead Institute for Biomedical Research (US)
- University College London (GB)
- Massachusetts Institute of Technology (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-08-19
- DOI
- https://doi.org/10.1038/s41467-026-76675-1
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Massachusetts Institute of Technology
- Fondation Brain Canada
- National Alliance for Research on Schizophrenia and Depression
- Simons Foundation Autism Research Initiative
- Stem Cell Network
- Canada Research Chairs
- University of Toronto
- Krembil Foundation
- Azrieli Foundation
- Hospital for Sick Children
- Department of Psychiatry, University of Toronto
- Canadian Institutes of Health Research
- Natural Sciences and Engineering Research Council of Canada
- National Institute of General Medical Sciences