Arseni D, Chen R, Murzin AG, Peak-Chew SY, Garringer HJ, Newell KL, Kametani F, Robinson AC, Vidal R, Ghetti B, Hasegawa M, Ryskeldi-Falcon B. TDP-43 forms amyloid filaments with a distinct fold in type A FTLD-TDP. Nature. 2023 Aug;620(7975):898-903. Epub 2023 Aug 2 PubMed.

Recommends

Please login to recommend the paper.

Comments

  1. Benjamin Ryskeldi-Falcon, Diane Arseni, and colleagues have extended their fantastic cryo-EM work in TDP-43 proteinopathies. After reporting the first structure of TDP-43 filaments in ALS/FTLD-TDP type B cases last year (Arseni et al., 2022), in this study they now resolved the structure(s) of TDP-43 filaments in FTLD-TDP type A cases. Importantly, the filaments in FTLD-TDP type A and B are structurally different, thereby providing the first direct evidence for the presence of distinct TDP-43 conformations.

    Since initial reports in 2006, subclassification of FTLD-TDP based on the pattern of neocortical TDP-43 pathology, with each subtype showing specific clinical and genetic correlations, became widely accepted in the field (Mackenzie et al., 2009; Mackenzie and Neumann, 2017).

    By analogy to other neurodegenerative diseases, a popular hypothesis to explain the heterogeneity in FTLD-TDP is to propose the presence of different conformational types of misfolded TDP-43, or “TDP-43 strains”, with each strain associated with specific cell tropism, seeding activity, and toxicity. While there was already growing, indirect evidence supporting the idea of distinct conformational TDP-43 species, with demonstration of biochemical differences of insoluble TDP-43 as well as identification of type-specific TDP-43 antibodies (reviewed in Neumann et al., 2021), this important study now provides the direct proof for different TDP-43 conformations as the likely molecular basis for the phenotypic variability among TDP-43 proteinopathies. I am very much looking forward to seeing the structure of FTLD-TDP type C filaments in the near future.

    References:

    Arseni D, Hasegawa M, Murzin AG, Kametani F, Arai M, Yoshida M, Ryskeldi-Falcon B. Structure of pathological TDP-43 filaments from ALS with FTLD. Nature. 2022 Jan;601(7891):139-143. Epub 2021 Dec 8 PubMed.

    Mackenzie IR, Neumann M, Bigio EH, Cairns NJ, Alafuzoff I, Kril J, Kovacs GG, Ghetti B, Halliday G, Holm IE, Ince PG, Kamphorst W, Revesz T, Rozemuller AJ, Kumar-Singh S, Akiyama H, Baborie A, Spina S, Dickson DW, Trojanowski JQ, Mann DM. Nomenclature for neuropathologic subtypes of frontotemporal lobar degeneration: consensus recommendations. Acta Neuropathol. 2009 Jan;117(1):15-8. PubMed.

    Mackenzie IR, Neumann M. Reappraisal of TDP-43 pathology in FTLD-U subtypes. Acta Neuropathol. 2017 Jul;134(1):79-96. Epub 2017 May 2 PubMed.

    Neumann M, Lee EB, Mackenzie IR. Frontotemporal Lobar Degeneration TDP-43-Immunoreactive Pathological Subtypes: Clinical and Mechanistic Significance. Adv Exp Med Biol. 2021;1281:201-217. PubMed.

    View all comments by Manuela Neumann

  2. The twists and turns of TDP

    The argument regarding whether the presence of specific fibrils in particular cases stems from different extraction procedures or case-specific neuropathological conditions seems to find support from both sides. This study led by Ryskeldi-Falcon describes the cryo-EM structure of TDP-43 filaments found in three patients with FTLD type A. These filaments exhibit a distinct five-layered core protofilament folded into a chevron-like shape, unlike the previously observed double spiral fold among individuals with FTLD/ALS (Arseni et al., 2022). Also, cryo-EM images reveal the presence of both single and double TMEM106B filaments in each individual.

    However, the presence of both TDP-43 filaments and TMEM106B filaments in type A FTLD-TDP and type B FTLD-TDP (Schweighauser et al., 2022) contradicts a recent report (Jiang et al., 2022) which showed that amyloid filaments in FTLD-TDP are composed of TMEM106B along with abundant non-fibrillar aggregated TDP-43, but not TDP-43 fibrils. The authors of the current report argue that differences in brain extraction protocols could explain this discrepancy. They found TDP43 filaments in the supernatant after centrifugation at 27,000 g, while the other study examined the pellet after centrifugation at 21,000 g. This is analogous to the discovery of abundant Aβ fibrils in ultracentrifugal supernatants of aqueous extracts from Alzheimer's disease brains (Stern et al., 2023). 

    The question then arises whether "purified" small aggregates or "protofibrils" from globular co-aggregates with other proteins inhibiting fibrillation can indeed form fibrils in the supernatant fraction. TDP may exhibit two distinct behaviors: N-terminus intact TDP has a high propensity to form functional oligomers-dimers that bind nucleic acids through RNA binding motifs, yet can misfold to generate globular aggregates, or co-aggregates, found in the pellets. In contrast, the amyloidogenic C-terminal (N-truncated) TDP forms “abundant” filaments found in the supernatant.

    Another significant point of the current study is that individual filaments exhibit heterogeneity, and uniform repetitive structures are not always assembled. Various local structural variations could coexist within individual filaments. Importantly, this study and that of Kumar et al., 2023, highlights the role of post-translational modifications (PTMs) in shaping the local structural variation of TDP-43 filaments. These modifications determine the preferred structural form of the filament structure, indicating that PTMs occurring prior to fibrillization, and influenced by different neurodegenerative conditions, ultimately dictate the final fold of the filaments.

    This concept is also applicable to other intrinsically disordered proteins, such as Aβ and tau. Thus, this suggests a broader concept where specific, disease-related PTM patterns determine the amyloid filament conformation of distinct proteins in neurodegenerative diseases.

    References:

    Arseni D, Hasegawa M, Murzin AG, Kametani F, Arai M, Yoshida M, Ryskeldi-Falcon B. Structure of pathological TDP-43 filaments from ALS with FTLD. Nature. 2022 Jan;601(7891):139-143. Epub 2021 Dec 8 PubMed.

    Jiang YX, Cao Q, Sawaya MR, Abskharon R, Ge P, DeTure M, Dickson DW, Fu JY, Ogorzalek Loo RR, Loo JA, Eisenberg DS. Amyloid fibrils in FTLD-TDP are composed of TMEM106B and not TDP-43. Nature. 2022 May;605(7909):304-309. Epub 2022 Mar 28 PubMed.

    Kumar ST, Nazarov S, Porta S, Maharjan N, Cendrowska U, Kabani M, Finamore F, Xu Y, Lee VM, Lashuel HA. Seeding the aggregation of TDP-43 requires post-fibrillization proteolytic cleavage. Nat Neurosci. 2023 Jun;26(6):983-996. Epub 2023 May 29 PubMed.

    Schweighauser M, Arseni D, Bacioglu M, Huang M, Lövestam S, Shi Y, Yang Y, Zhang W, Kotecha A, Garringer HJ, Vidal R, Hallinan GI, Newell KL, Tarutani A, Murayama S, Miyazaki M, Saito Y, Yoshida M, Hasegawa K, Lashley T, Revesz T, Kovacs GG, van Swieten J, Takao M, Hasegawa M, Ghetti B, Spillantini MG, Ryskeldi-Falcon B, Murzin AG, Goedert M, Scheres SH. Age-dependent formation of TMEM106B amyloid filaments in human brains. Nature. 2022 May;605(7909):310-314. Epub 2022 Mar 28 PubMed.

    Stern AM, Yang Y, Jin S, Yamashita K, Meunier AL, Liu W, Cai Y, Ericsson M, Liu L, Goedert M, Scheres SH, Selkoe DJ. Abundant Aβ fibrils in ultracentrifugal supernatants of aqueous extracts from Alzheimer's disease brains. Neuron. 2023 Jul 5;111(13):2012-2020.e4. Epub 2023 May 10 PubMed.

    View all comments by Victor Streltsov

  3. This manuscript by the Ryskeldi-Falcon lab clarifies several important issues. It is clear now that TDP-43 forms amyloid fibers in FTLD Type A and Type B—and, as in other neurodegenerative diseases, these fibers show distinct structures and are therefore disease defining. The unambiguous presence of TDP-43 filaments in both FTLD-TDP type A and B further supports the pathological nature of these aggregates. Most importantly, the findings in this paper, as well as in the earlier publication (Arseni et al., 2022), provide a basis for the development of disease-specific diagnostics and therapeutics.

    Importantly, these findings are in contrast to previous observations that amyloid fibers in FTLD-TDP were composed solely of TMEM106B, but not of TDP-43 (Jiang et al., 2022). 

    But what about a pathological contribution of the TMEM106B deposits, if any? Their ubiquitous detection in many different neurodegenerative disorders, and their age-dependent occurrence even in neurologically normal humans, suggest that they are either innocent bystanders or that they enhance the risk for many different neurodegenerative diseases by an unknown mechanism.

    The rather ubiquitous occurrence of the TMEM106B deposits in many neurological conditions would suggest a disease-overarching mechanism. Based on the age-dependent occurrence of the TMEM106B deposits, I could imagine that they may contribute to disease risk by affecting age-related processes in the brain and therefore facilitate earlier disease onset. One possibility is that the TMEM106B fibers arise in dysfunctional endosomes/lysosomes and may then even further reduce lysosomal function. Over time, this may then lead to disruption of lysosomes and leakage of lysosomal content into the cytoplasm.  

    References:

    Arseni D, Hasegawa M, Murzin AG, Kametani F, Arai M, Yoshida M, Ryskeldi-Falcon B. Structure of pathological TDP-43 filaments from ALS with FTLD. Nature. 2022 Jan;601(7891):139-143. Epub 2021 Dec 8 PubMed.

    Jiang YX, Cao Q, Sawaya MR, Abskharon R, Ge P, DeTure M, Dickson DW, Fu JY, Ogorzalek Loo RR, Loo JA, Eisenberg DS. Amyloid fibrils in FTLD-TDP are composed of TMEM106B and not TDP-43. Nature. 2022 May;605(7909):304-309. Epub 2022 Mar 28 PubMed.

    View all comments by Christian Haass

  4. In this important analysis, Arseni et al. build on their previous work. They demonstrate that the fibrils underpinning the two most common TDP-43 subtypes are composed of distinct folds of the same LCD region—chevron-like in type A and spiral-like in type B—of which the former may have been facilitated by post-translational modifications of arginine 293.

    These findings provide structural support for the pathological distinction of FTLD-TDP types A and B, which are often the most difficult to differentiate, even by the most experienced neuropathologists (Alafuzoff et al., 2015). It would be interesting to know whether the filament folds of TDP-43 in ALS are indeed the same as those described in FTLD-ALS TDP type B, and if this differs from type E, which has a more distinctive morphology, distribution, and spread compared to types A and B (Porta et al., 2021), and which we have found more commonly represented in ALS cases without FTLD.

    View all comments by Rachel Tan

  5. This manuscript consolidates previous findings by the same group that TDP-43 can form filaments with β-strands that stack in a parallel, in-register arrangement (chevron fold), although with a different fold with respect to the previously described filaments (double-spiral-shaped fold). It removes doubts that previously found filaments reported by the same group last year (Arseni et al., 2022) derived from the TMEM106B protein.

    Benjamin Ryskeldi-Falcon, whom I had the pleasure of contacting last year to discuss this specific point, was well aware of the presence of TMEM106b fibrils in the elderly and ruled out, after his first Nature paper was released in 2022, that his TDP-43 filaments consisted of TMEM106B fibrils.

    A doubt remains that many of the TDP-43 inclusions may not have filaments altogether, particularly the round inclusions, as opposed to the skein-like inclusions. Robinson et al. in 2013 had noticed that only a limited subset of TDP-43 skein-like inclusions could bind weakly Thioflavin S, whereas none of the round inclusions did. Papers by Jiang et al. and Laferrière et al. in Nature and Nature Neuroscience in 2022 and 2016, respectively, showed absence of TDP-43 filaments. I saw comments that this may arise from the different extraction procedures, but I wonder whether this is due to the polymorphism in TDP-43 aggregation that lead to non-filamentous structure in many of the cases, as well as different folds when filaments do form.

    We indeed had trouble generating filamentous structures by expressing TDP-43 in cells or from the purified protein, indicating its low propensity to form amyloid filaments (Cascella et al., 2023). 

    It's also important to discuss that neither of the TDP-43 filament folds described in 2022 and 2023 possess a clear stacking of β-sheets along an axis perpendicular to the major filament axis. In X-ray fiber diffraction of oriented fibrils, the TDP-43 filaments would show the 4.7 Å reflection on the meridional axis, but not the 10-11 Å reflection on the equatorial axis, which has been used in the past to classify aggregated fibrils as amyloid. Absence of thioflavin S/T binding also represents a departure from classical fibrils.

    References:

    Arseni D, Hasegawa M, Murzin AG, Kametani F, Arai M, Yoshida M, Ryskeldi-Falcon B. Structure of pathological TDP-43 filaments from ALS with FTLD. Nature. 2022 Jan;601(7891):139-143. Epub 2021 Dec 8 PubMed.

    Jiang YX, Cao Q, Sawaya MR, Abskharon R, Ge P, DeTure M, Dickson DW, Fu JY, Ogorzalek Loo RR, Loo JA, Eisenberg DS. Amyloid fibrils in FTLD-TDP are composed of TMEM106B and not TDP-43. Nature. 2022 May;605(7909):304-309. Epub 2022 Mar 28 PubMed.

    Laferrière F, Maniecka Z, Pérez-Berlanga M, Hruska-Plochan M, Gilhespy L, Hock EM, Wagner U, Afroz T, Boersema PJ, Barmettler G, Foti SC, Asi YT, Isaacs AM, Al-Amoudi A, Lewis A, Stahlberg H, Ravits J, De Giorgi F, Ichas F, Bezard E, Picotti P, Lashley T, Polymenidou M. TDP-43 extracted from frontotemporal lobar degeneration subject brains displays distinct aggregate assemblies and neurotoxic effects reflecting disease progression rates. Nat Neurosci. 2019 Jan;22(1):65-77. Epub 2018 Dec 17 PubMed.

    Robinson JL, Geser F, Stieber A, Umoh M, Kwong LK, Van Deerlin VM, Lee VM, Trojanowski JQ. TDP-43 skeins show properties of amyloid in a subset of ALS cases. Acta Neuropathol. 2013 Jan;125(1):121-31. PubMed.

    Cascella R, Banchelli M, Abolghasem Ghadami S, Ami D, Gagliani MC, Bigi A, Staderini T, Tampellini D, Cortese K, Cecchi C, Natalello A, Adibi H, Matteini P, Chiti F. An in situ and in vitro investigation of cytoplasmic TDP-43 inclusions reveals the absence of a clear amyloid signature. Ann Med. 2023 Dec;55(1):72-88. PubMed.

    View all comments by Fabrizio Chiti

Make a Comment

To make a comment you must login or register.

This paper appears in the following:

News

  1. In Frontotemporal Lobar Dementia, TDP-43 Snaps into a Chevron Shape