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Longhini AP, DuBose A, Lobo S, Vijayan V, Bai Y, Rivera EK, Sala-Jarque J, Nikitina A, Carrettiero DC, Unger MT, Sclafani OR, Fu V, Beckett ER, Vigers M, Buée L, Landrieu I, Shell S, Shea JE, Han S, Kosik KS. Precision proteoform design for 4R tau isoform selective templated aggregation. Proc Natl Acad Sci U S A 2024; 121:e2320456121. [PMID: 38568974 PMCID: PMC11009657 DOI: 10.1073/pnas.2320456121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024] Open
Abstract
Prion-like spread of disease-specific tau conformers is a hallmark of all tauopathies. A 19-residue probe peptide containing a P301L mutation and spanning the R2/R3 splice junction of tau folds and stacks into seeding-competent fibrils and induces aggregation of 4R, but not 3R tau. These tau peptide fibrils propagate aggregated intracellular tau over multiple generations, have a high β-sheet content, a colocalized lipid signal, and adopt a well-defined U-shaped fold found in 4R tauopathy brain-derived fibrils. Fully atomistic replica exchange molecular dynamics (MD) simulations were used to compute the free energy landscapes of the conformational ensemble of the peptide monomers. These identified an aggregation-prohibiting β-hairpin structure and an aggregation-competent U-fold unique to 4R tauopathy fibrils. Guided by MD simulations, we identified that the N-terminal-flanking residues to PHF6, which slightly vary between 4R and 3R isoforms, modulate seeding. Strikingly, when a single amino acid switch at position 305 replaced the serine of 4R tau with a lysine from the corresponding position in the first repeat of 3R tau, the seeding induced by the 19-residue peptide was markedly reduced. Conversely, a 4R tau mimic with three repeats, prepared by replacing those amino acids in the first repeat with those amino acids uniquely present in the second repeat, recovered aggregation when exposed to the 19-residue peptide. These peptide fibrils function as partial prions to recruit naive 4R tau-ten times the length of the peptide-and serve as a critical template for 4R tauopathy propagation. These results hint at opportunities for tau isoform-specific therapeutic interventions.
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Affiliation(s)
- Andrew P. Longhini
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Austin DuBose
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
| | - Samuel Lobo
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA93106
| | - Vishnu Vijayan
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
| | - Yeran Bai
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
- Photothermal Spectroscopy Corp., Santa Barbara, CA93101
| | - Erica Keane Rivera
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Julia Sala-Jarque
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Arina Nikitina
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Daniel C. Carrettiero
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, São Paulo09600-000, Brazil
| | - Matthew T. Unger
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Olivia R. Sclafani
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Valerie Fu
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Emily R. Beckett
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Michael Vigers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
| | - Luc Buée
- University of Lille, Inserm, CHU Lille, Lille Neuroscience & CognitionLilleF-59000, France
- Laboratoire d'Excellence Development of Innovative Strategies for a Transdisciplinary Approach to Alzheimer's Disease, Alzheimer & Tauopathies Team, LilleF-59000, France
| | - Isabelle Landrieu
- Center National de la Recherche Scientifique Équipe de Recherche 9002–Integrative Structural Biology, LilleF-59000, France
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1167–Risk Factors and Molecular Determinants of Aging-Related DiseasesLilleF-59000, France
| | - Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA93106
| | - Joan E. Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA93106
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA93106
| | - Kenneth S. Kosik
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
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Almeida MC, Eger SJ, He C, Audouard M, Nikitina A, Glasauer SMK, Han D, Mejía-Cupajita B, Acosta-Uribe J, Villalba-Moreno ND, Littau JL, Elcheikhali M, Rivera EK, Carrettiero DC, Villegas-Lanau CA, Sepulveda-Falla D, Lopera F, Kosik KS. Single-nucleus RNA sequencing demonstrates an autosomal dominant Alzheimer's disease profile and possible mechanisms of disease protection. Neuron 2024:S0896-6273(24)00093-X. [PMID: 38417436 DOI: 10.1016/j.neuron.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 01/07/2024] [Accepted: 02/09/2024] [Indexed: 03/01/2024]
Abstract
Highly penetrant autosomal dominant Alzheimer's disease (ADAD) comprises a distinct disease entity as compared to the far more prevalent form of AD in which common variants collectively contribute to risk. The downstream pathways that distinguish these AD forms in specific cell types have not been deeply explored. We compared single-nucleus transcriptomes among a set of 27 cases divided among PSEN1-E280A ADAD carriers, sporadic AD, and controls. Autophagy genes and chaperones clearly defined the PSEN1-E280A cases compared to sporadic AD. Spatial transcriptomics validated the activation of chaperone-mediated autophagy genes in PSEN1-E280A. The PSEN1-E280A case in which much of the brain was spared neurofibrillary pathology and harbored a homozygous APOE3-Christchurch variant revealed possible explanations for protection from AD pathology including overexpression of LRP1 in astrocytes, increased expression of FKBP1B, and decreased PSEN1 expression in neurons. The unique cellular responses in ADAD and sporadic AD require consideration when designing clinical trials.
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Affiliation(s)
- Maria Camila Almeida
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Center for Natural and Humans Sciences, Federal University of ABC, Sao Bernardo do Campo, SP 09608020, Brazil
| | - Sarah J Eger
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Caroline He
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Morgane Audouard
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Arina Nikitina
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stella M K Glasauer
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Dasol Han
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Barbara Mejía-Cupajita
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia
| | - Juliana Acosta-Uribe
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia
| | - Nelson David Villalba-Moreno
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jessica Lisa Littau
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Megan Elcheikhali
- Department of Statistics and Applied Probability, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Erica Keane Rivera
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Daniel Carneiro Carrettiero
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Center for Natural and Humans Sciences, Federal University of ABC, Sao Bernardo do Campo, SP 09608020, Brazil
| | | | - Diego Sepulveda-Falla
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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3
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Longhini AP, DuBose A, Lobo S, Vijayan V, Bai Y, Rivera EK, Sala-Jarque J, Nikitina A, Carrettiero DC, Unger M, Sclafani O, Fu V, Vigers M, Buee L, Landrieu I, Shell S, Shea JE, Han S, Kosik KS. Precision Proteoform Design for 4R Tau Isoform Selective Templated Aggregation. bioRxiv 2023:2023.08.31.555649. [PMID: 37693456 PMCID: PMC10491155 DOI: 10.1101/2023.08.31.555649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Prion-like spread of disease-specific tau conformers is a hallmark of all tauopathies. A 19-residue probe peptide containing a P301L mutation and spanning the R2/R3 splice junction of tau, folds and stacks into seeding-competent fibrils and induces aggregation of 4R, but not 3R tau. These tau peptide fibrils propagate aggregated intracellular tau over multiple generations, have a high β-sheet content, a colocalized lipid signal, and adopt a well-defined U-shaped fold found in 4R tauopathy brain-derived fibrils. Fully atomistic replica exchange molecular dynamics (MD) simulations were used to compute the free energy landscapes of the conformational ensemble of the peptide monomers. These identified an aggregation-prohibiting β-hairpin structure and an aggregation-competent U-fold unique to 4R tauopathy fibrils. Guided by MD simulations, we identified that the N-terminal-flanking residues to PHF6, which slightly vary between 4R and 3R isoforms, modulate seeding. Strikingly, when a single amino acid switch at position 305 replaced the serine of 4R tau with a lysine from the corresponding position in the first repeat of 3R tau, the seeding induced by the 19-residue peptide was markedly reduced. Conversely, a 4R tau mimic with three repeats, prepared by replacing those amino acids in the first repeat with those amino acids uniquely present in the second repeat, recovered aggregation when exposed to the 19-residue peptide. These peptide fibrils function as partial prions to recruit naïve 4R tau-ten times the length of the peptide-and serve as a critical template for 4R tauopathy propagation. These results hint at opportunities for tau isoform-specific therapeutic interventions.
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Affiliation(s)
- Andrew P. Longhini
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Austin DuBose
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
| | - Samuel Lobo
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Vishnu Vijayan
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
| | - Yeran Bai
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
- Photothermal Spectroscopy Corp., Santa Barbara, CA 93101, USA
| | - Erica Keane Rivera
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Julia Sala-Jarque
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Arina Nikitina
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Daniel C. Carrettiero
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, Brazil
| | - Matthew Unger
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Olivia Sclafani
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Valerie Fu
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Michael Vigers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
| | - Luc Buee
- Univ. Lille, Inserm, CHU Lille, LilNCog – Lille Neuroscience & Cognition, F-59000 Lille, France
- LabEx DISTALZ, Alzheimer & Tauopathies Team, F-59000 Lille, France
| | - Isabelle Landrieu
- CNRS EMR9002 – BSI - Integrative Structural Biology F-59000 Lille, France
| | - Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Joan E. Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France. Department of Physics, University of California, Santa Barbara, Santa Barbara, CA
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Lead Contacts
| | - Kenneth S. Kosik
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
- Lead Contacts
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