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Smukowski SN, Danyko C, Somberg J, Kaufman EJ, Course MM, Postupna N, Barker-Haliski M, Keene CD, Valdmanis PN. mRNA and circRNA mislocalization to synapses are key features of Alzheimer's disease. PLoS Genet 2024; 20:e1011359. [PMID: 39074152 PMCID: PMC11309398 DOI: 10.1371/journal.pgen.1011359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/08/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
Proper transport of RNAs to synapses is essential for localized translation of proteins in response to synaptic signals and synaptic plasticity. Alzheimer's disease (AD) is a neurodegenerative disease characterized by accumulation of amyloid aggregates and hyperphosphorylated tau neurofibrillary tangles followed by widespread synapse loss. To understand whether RNA synaptic localization is impacted in AD, we performed RNA sequencing on synaptosomes and brain homogenates from AD patients and cognitively healthy controls. This resulted in the discovery of hundreds of mislocalized mRNAs in AD among frontal and temporal brain regions. Similar observations were found in an APPswe/PSEN1dE9 mouse model. Furthermore, major differences were observed among circular RNAs (circRNAs) localized to synapses in AD including two overlapping isoforms of circGSK3β, one upregulated, and one downregulated. Expression of these distinct isoforms affected tau phosphorylation in neuronal cells substantiating the importance of circRNAs in the brain and pointing to a new class of therapeutic targets.
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Affiliation(s)
- Samuel N. Smukowski
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Cassidy Danyko
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Fred Hutch Cancer Center, Basic Sciences Division, University of Washington, Seattle, Washington, United States of America
| | - Jenna Somberg
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Eli J. Kaufman
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Meredith M. Course
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Nadia Postupna
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Melissa Barker-Haliski
- Department of Pharmacy, University of Washington School of Pharmacy, Seattle, Washington, United States of America
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Paul N. Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
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Gouveia Roque C, Phatnani H, Hengst U. The broken Alzheimer's disease genome. CELL GENOMICS 2024; 4:100555. [PMID: 38697121 PMCID: PMC11099344 DOI: 10.1016/j.xgen.2024.100555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/25/2024] [Accepted: 04/07/2024] [Indexed: 05/04/2024]
Abstract
The complex pathobiology of late-onset Alzheimer's disease (AD) poses significant challenges to therapeutic and preventative interventions. Despite these difficulties, genomics and related disciplines are allowing fundamental mechanistic insights to emerge with clarity, particularly with the introduction of high-resolution sequencing technologies. After all, the disrupted processes at the interface between DNA and gene expression, which we call the broken AD genome, offer detailed quantitative evidence unrestrained by preconceived notions about the disease. In addition to highlighting biological pathways beyond the classical pathology hallmarks, these advances have revitalized drug discovery efforts and are driving improvements in clinical tools. We review genetic, epigenomic, and gene expression findings related to AD pathogenesis and explore how their integration enables a better understanding of the multicellular imbalances contributing to this heterogeneous condition. The frontiers opening on the back of these research milestones promise a future of AD care that is both more personalized and predictive.
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Affiliation(s)
- Cláudio Gouveia Roque
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA; Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY 10032, USA
| | - Ulrich Hengst
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Pathology & Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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Konopka G, Bhaduri A. Functional genomics and systems biology in human neuroscience. Nature 2023; 623:274-282. [PMID: 37938705 DOI: 10.1038/s41586-023-06686-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/27/2023] [Indexed: 11/09/2023]
Abstract
Neuroscience research has entered a phase of key discoveries in the realm of neurogenomics owing to strong financial and intellectual support for resource building and tool development. The previous challenge of tissue heterogeneity has been met with the application of techniques that can profile individual cells at scale. Moreover, the ability to perturb genes, gene regulatory elements and neuronal activity in a cell-type-specific manner has been integrated with gene expression studies to uncover the functional underpinnings of the genome at a systems level. Although these insights have necessarily been grounded in model systems, we now have the opportunity to apply these approaches in humans and in human tissue, thanks to advances in human genetics, brain imaging and tissue collection. We acknowledge that there will probably always be limits to the extent to which we can apply the genomic tools developed in model systems to human neuroscience; however, as we describe in this Perspective, the neuroscience field is now primed with an optimal foundation for tackling this ambitious challenge. The application of systems-level network analyses to these datasets will facilitate a deeper appreciation of human neurogenomics that cannot otherwise be achieved from directly observable phenomena.
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Affiliation(s)
- Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- Peter O'Donnell Jr Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA.
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Niu M, Zong C. Reply to: Methodological concerns and lack of evidence for single-synapse RNA-seq. Nat Biotechnol 2023; 41:1225-1228. [PMID: 37500916 DOI: 10.1038/s41587-023-01878-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Affiliation(s)
- Muchun Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- McNair Medical Institute, Baylor College of Medicine, Houston, TX, USA.
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