Cryo-EM structures of amyloid-β 42 filaments from human brains

Alzheimer’s disease is characterized by a loss of memory and other cognitive functions and the filamentous assembly of Aβ and tau in the brain. The assembly of Aβ peptides into filaments that end at residue 42 is a central event. Yang et al. used electron cryo–electron microscopy to determine the structures of Aβ42 filaments from human brain (see the Perspective by Willem and Fändrich). They identified two types of related S-shaped filaments, each consisting of two identical protofilaments. These structures will inform the development of better in vitro and animal models, inhibitors of Aβ42 assembly, and imaging agents with increased specificity and sensitivity. —SM

TDP-43 forms amyloid filaments with a distinct fold in type A FTLD-TDP.

Acknowledgements: We thank the individuals and their families for donating brain tissue; the Manchester Brain Bank, which is part of the Brains for Dementia Research Initiative, jointly funded by the Alzheimer’s Society and Alzheimer’s Research UK, for supplying tissue from individuals 1 and 3; J. H. Grafman for supplying tissue from individual 4; the National Centralized Repository for Alzheimer’s Disease and Related Dementias, which receives funding from the National Institute on Aging, for supplying tissue from individual 5; the Center for Medical Genomics of Indiana University School of Medicine for next-generation DNA sequencing; M. H. Jacobsen for help with neuropathological examinations; R. Otani for help with immunolabelling; M. Tahira for help with mass spectrometry; K. Yamashita and G. Murshudov for help with Servalcat and model refinements in REFMAC5; staff at the MRC Laboratory of Molecular Biology Electron Microscopy Facility for access to and support with cryo-EM; staff at the MRC Laboratory of Molecular Biology Scientific Computing Facility for access to and support with computing; staff at the MRC Laboratory of Molecular Biology Mass Spectrometry Facility for access to and support with mass spectrometry; and T.S. Behr, A. Bertolotti, S.W. Davies, M. Goedert, S.H.W. Scheres and S. Tetter for discussions. This work was supported by the Medical Research Council, as part of UK Research and Innovation (MC_UP_1201/25 to B.R.-F.); an Alzheimer’s Research UK Rising Star Award (ARUK-RS2019-001 to B.R.-F.); the US National Institutes of Health (P30-AG010133, U01-NS110437 and RF1-AG071177 to R.V. and B.G); the Japan Agency for Medical Research and Development (JP20dm0207072 to M.H.); the Japan Science and Technology Agency Core Research for Evolutional Science and Technology (JPMJCR18H3 to M.H.); a Cambridge Commonwealth, European & International Trust Postgraduate Scholarship to R.C.; and a Leverhulme Early Career Fellowship (ECF-2022-610 to D.A.). For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author-accepted manuscript version arising.The abnormal assembly of TAR DNA-binding protein 43 (TDP-43) in neuronal and glial cells characterizes nearly all cases of amyotrophic lateral sclerosis (ALS) and around half of cases of frontotemporal lobar degeneration (FTLD)1,2. A causal role for TDP-43 assembly in neurodegeneration is evidenced by dominantly inherited missense mutations in TARDBP, the gene encoding TDP-43, that promote assembly and give rise to ALS and FTLD3-7. At least four types (A-D) of FTLD with TDP-43 pathology (FTLD-TDP) are defined by distinct brain distributions of assembled TDP-43 and are associated with different clinical presentations of frontotemporal dementia8. We previously showed, using cryo-electron microscopy, that TDP-43 assembles into amyloid filaments in ALS and type B FTLD-TDP9. However, the structures of assembled TDP-43 in FTLD without ALS remained unknown. Here we report the cryo-electron microscopy structures of assembled TDP-43 from the brains of three individuals with the most common type of FTLD-TDP, type A. TDP-43 formed amyloid filaments with a new fold that was the same across individuals, indicating that this fold may characterize type A FTLD-TDP. The fold resembles a chevron badge and is unlike the double-spiral-shaped fold of ALS and type B FTLD-TDP, establishing that distinct filament folds of TDP-43 characterize different neurodegenerative conditions. The structures, in combination with mass spectrometry, led to the identification of two new post-translational modifications of assembled TDP-43, citrullination and monomethylation of R293, and indicate that they may facilitate filament formation and observed structural variation in individual filaments. The structures of TDP-43 filaments from type A FTLD-TDP will guide mechanistic studies of TDP-43 assembly, as well as the development of diagnostic and therapeutic compounds for TDP-43 proteinopathies

TDP-43 forms amyloid filaments with a distinct fold in type A FTLD-TDP

Acknowledgements: We thank the individuals and their families for donating brain tissue; the Manchester Brain Bank, which is part of the Brains for Dementia Research Initiative, jointly funded by the Alzheimer’s Society and Alzheimer’s Research UK, for supplying tissue from individuals 1 and 3; J. H. Grafman for supplying tissue from individual 4; the National Centralized Repository for Alzheimer’s Disease and Related Dementias, which receives funding from the National Institute on Aging, for supplying tissue from individual 5; the Center for Medical Genomics of Indiana University School of Medicine for next-generation DNA sequencing; M. H. Jacobsen for help with neuropathological examinations; R. Otani for help with immunolabelling; M. Tahira for help with mass spectrometry; K. Yamashita and G. Murshudov for help with Servalcat and model refinements in REFMAC5; staff at the MRC Laboratory of Molecular Biology Electron Microscopy Facility for access to and support with cryo-EM; staff at the MRC Laboratory of Molecular Biology Scientific Computing Facility for access to and support with computing; staff at the MRC Laboratory of Molecular Biology Mass Spectrometry Facility for access to and support with mass spectrometry; and T.S. Behr, A. Bertolotti, S.W. Davies, M. Goedert, S.H.W. Scheres and S. Tetter for discussions. This work was supported by the Medical Research Council, as part of UK Research and Innovation (MC_UP_1201/25 to B.R.-F.); an Alzheimer’s Research UK Rising Star Award (ARUK-RS2019-001 to B.R.-F.); the US National Institutes of Health (P30-AG010133, U01-NS110437 and RF1-AG071177 to R.V. and B.G); the Japan Agency for Medical Research and Development (JP20dm0207072 to M.H.); the Japan Science and Technology Agency Core Research for Evolutional Science and Technology (JPMJCR18H3 to M.H.); a Cambridge Commonwealth, European & International Trust Postgraduate Scholarship to R.C.; and a Leverhulme Early Career Fellowship (ECF-2022-610 to D.A.). For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author-accepted manuscript version arising.The abnormal assembly of TAR DNA-binding protein 43 (TDP-43) in neuronal and glial cells characterizes nearly all cases of amyotrophic lateral sclerosis (ALS) and around half of cases of frontotemporal lobar degeneration (FTLD)1, 2. A causal role for TDP-43 assembly in neurodegeneration is evidenced by dominantly inherited missense mutations in TARDBP, the gene encoding TDP-43, that promote assembly and give rise to ALS and FTLD3–7. At least four types (A–D) of FTLD with TDP-43 pathology (FTLD-TDP) are defined by distinct brain distributions of assembled TDP-43 and are associated with different clinical presentations of frontotemporal dementia8. We previously showed, using cryo-electron microscopy, that TDP-43 assembles into amyloid filaments in ALS and type B FTLD-TDP9. However, the structures of assembled TDP-43 in FTLD without ALS remained unknown. Here we report the cryo-electron microscopy structures of assembled TDP-43 from the brains of three individuals with the most common type of FTLD-TDP, type A. TDP-43 formed amyloid filaments with a new fold that was the same across individuals, indicating that this fold may characterize type A FTLD-TDP. The fold resembles a chevron badge and is unlike the double-spiral-shaped fold of ALS and type B FTLD-TDP, establishing that distinct filament folds of TDP-43 characterize different neurodegenerative conditions. The structures, in combination with mass spectrometry, led to the identification of two new post-translational modifications of assembled TDP-43, citrullination and monomethylation of R293, and indicate that they may facilitate filament formation and observed structural variation in individual filaments. The structures of TDP-43 filaments from type A FTLD-TDP will guide mechanistic studies of TDP-43 assembly, as well as the development of diagnostic and therapeutic compounds for TDP-43 proteinopathies

TAF15 amyloid filaments in frontotemporal lobar degeneration.

Acknowledgements: We thank the individuals and their families for donating brain tissue; the Queen Square Brain Bank for Neurological Disorders at University College London Queen Square Institute of Neurology, which receives support from the Reta Lila Weston Institute for Neurological Studies, for supplying tissue from individuals 2 and 3; J. Grafman for supplying tissue from individual 4; M. Jacobsen for help with neuropathological examinations; R. Richardson, K. Cox and N. Maynard for help with histology and immunohistochemistry; J. Grimmett, T. Darling and I. Clayson for help with high-performance computing; K. Yamashita and G. Murshudov for help with model refinements; and T. Behr, A. Bertolotti, R. Chen, S. Davies, M. Goedert, D. Hilvert and S. Scheres for discussions. This work was supported by the electron microscopy and scientific computing facilities at the MRC Laboratory of Molecular Biology and by the Center for Medical Genomics at the Indiana University School of Medicine. This work was supported by the Medical Research Council as part of United Kingdom Research and Innovation (also known as UK Research and Innovation) (no. MC_UP_1201/25 to B.R.-F.); the US National Institutes of Health (nos. U01-NS110437, RF1-AG071177 and R01-AG080001 to R.V. and B.G.); the Alzheimer’s Society (nos. AS-PG-18-004 and AS-PG-21-004 to T.L.); the Association for Frontotemporal Degeneration (no. 2019-0009 to Y.B. and T.L.); a Swiss National Science Foundation Postdoctoral Fellowship (no. P500PB_206890 to S.T.); and a Leverhulme Early Career Fellowship (no. ECF-2022-610 to D.A.). For the purposes of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising.Frontotemporal lobar degeneration (FTLD) causes frontotemporal dementia (FTD), the most common form of dementia after Alzheimer's disease, and is often also associated with motor disorders1. The pathological hallmarks of FTLD are neuronal inclusions of specific, abnormally assembled proteins2. In the majority of cases the inclusions contain amyloid filament assemblies of TAR DNA-binding protein 43 (TDP-43) or tau, with distinct filament structures characterizing different FTLD subtypes3,4. The presence of amyloid filaments and their identities and structures in the remaining approximately 10% of FTLD cases are unknown but are widely believed to be composed of the protein fused in sarcoma (FUS, also known as translocated in liposarcoma). As such, these cases are commonly referred to as FTLD-FUS. Here we used cryogenic electron microscopy (cryo-EM) to determine the structures of amyloid filaments extracted from the prefrontal and temporal cortices of four individuals with FTLD-FUS. Surprisingly, we found abundant amyloid filaments of the FUS homologue TATA-binding protein-associated factor 15 (TAF15, also known as TATA-binding protein-associated factor 2N) rather than of FUS itself. The filament fold is formed from residues 7-99 in the low-complexity domain (LCD) of TAF15 and was identical between individuals. Furthermore, we found TAF15 filaments with the same fold in the motor cortex and brainstem of two of the individuals, both showing upper and lower motor neuron pathology. The formation of TAF15 amyloid filaments with a characteristic fold in FTLD establishes TAF15 proteinopathy in neurodegenerative disease. The structure of TAF15 amyloid filaments provides a basis for the development of model systems of neurodegenerative disease, as well as for the design of diagnostic and therapeutic tools targeting TAF15 proteinopathy

Tau filaments from amyotrophic lateral sclerosis/parkinsonism-dementia complex adopt the CTE fold

Peer reviewed: TruePublication status: PublishedThe amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) of the island of Guam and the Kii peninsula of Japan is a fatal neurodegenerative disease of unknown cause that is characterized by the presence of abundant filamentous tau inclusions in brains and spinal cords. Here, we used electron cryo-microscopy to determine the structures of tau filaments from the cerebral cortex of three cases of ALS/PDC from Guam and eight cases from Kii, as well as from the spinal cord of two of the Guam cases. Tau filaments had the chronic traumatic encephalopathy (CTE) fold, with variable amounts of Type I and Type II filaments. Paired helical tau filaments were also found in three Kii cases and tau filaments with the corticobasal degeneration fold in one Kii case. We identified a new Type III CTE tau filament, where protofilaments pack against each other in an antiparallel fashion. ALS/PDC is the third known tauopathy with CTE-type filaments and abundant tau inclusions in cortical layers II/III, the others being CTE and subacute sclerosing panencephalitis. Because these tauopathies are believed to have environmental causes, our findings support the hypothesis that ALS/PDC is caused by exogenous factors.</jats:p

Tau filaments from amyotrophic lateral sclerosis/parkinsonism-dementia complex adopt the CTE fold.

Peer reviewed: TruePublication status: PublishedThe amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) of the island of Guam and the Kii peninsula of Japan is a fatal neurodegenerative disease of unknown cause that is characterized by the presence of abundant filamentous tau inclusions in brains and spinal cords. Here, we used electron cryo-microscopy to determine the structures of tau filaments from the cerebral cortex of three cases of ALS/PDC from Guam and eight cases from Kii, as well as from the spinal cord of two of the Guam cases. Tau filaments had the chronic traumatic encephalopathy (CTE) fold, with variable amounts of Type I and Type II filaments. Paired helical tau filaments were also found in three Kii cases and tau filaments with the corticobasal degeneration fold in one Kii case. We identified a new Type III CTE tau filament, where protofilaments pack against each other in an antiparallel fashion. ALS/PDC is the third known tauopathy with CTE-type filaments and abundant tau inclusions in cortical layers II/III, the others being CTE and subacute sclerosing panencephalitis. Because these tauopathies are believed to have environmental causes, our findings support the hypothesis that ALS/PDC is caused by exogenous factors

Age-dependent formation of TMEM106B amyloid filaments in human brains.

Many age-dependent neurodegenerative diseases, such as Alzheimer's and Parkinson's, are characterized by abundant inclusions of amyloid filaments. Filamentous inclusions of the proteins tau, amyloid-β, α-synuclein and transactive response DNA-binding protein (TARDBP; also known as TDP-43) are the most common1,2. Here we used structure determination by cryogenic electron microscopy to show that residues 120-254 of the lysosomal type II transmembrane protein 106B (TMEM106B) also form amyloid filaments in human brains. We determined the structures of TMEM106B filaments from a number of brain regions of 22 individuals with abundant amyloid deposits, including those resulting from sporadic and inherited tauopathies, amyloid-β amyloidoses, synucleinopathies and TDP-43 proteinopathies, as well as from the frontal cortex of 3 individuals with normal neurology and no or only a few amyloid deposits. We observed three TMEM106B folds, with no clear relationships between folds and diseases. TMEM106B filaments correlated with the presence of a 29-kDa sarkosyl-insoluble fragment and globular cytoplasmic inclusions, as detected by an antibody specific to the carboxy-terminal region of TMEM106B. The identification of TMEM106B filaments in the brains of older, but not younger, individuals with normal neurology indicates that they form in an age-dependent manner

Age-dependent formation of TMEM106B amyloid filaments in human brains

Many age-dependent neurodegenerative diseases, such as Alzheimer's and Parkinson's, are characterized by abundant inclusions of amyloid filaments. Filamentous inclusions of the proteins tau, amyloid-β, α-synuclein and transactive response DNA-binding protein (TARDBP; also known as TDP-43) are the most common1,2. Here we used structure determination by cryogenic electron microscopy to show that residues 120-254 of the lysosomal type II transmembrane protein 106B (TMEM106B) also form amyloid filaments in human brains. We determined the structures of TMEM106B filaments from a number of brain regions of 22 individuals with abundant amyloid deposits, including those resulting from sporadic and inherited tauopathies, amyloid-β amyloidoses, synucleinopathies and TDP-43 proteinopathies, as well as from the frontal cortex of 3 individuals with normal neurology and no or only a few amyloid deposits. We observed three TMEM106B folds, with no clear relationships between folds and diseases. TMEM106B filaments correlated with the presence of a 29-kDa sarkosyl-insoluble fragment and globular cytoplasmic inclusions, as detected by an antibody specific to the carboxy-terminal region of TMEM106B. The identification of TMEM106B filaments in the brains of older, but not younger, individuals with normal neurology indicates that they form in an age-dependent manner