Abstract

Main

TMEM106B is a type II transmembrane protein of 274 residues that localizes to late endosomes and lysosomes^3,4. It is expressed ubiquitously, with the highest levels in the brain, heart, thyroid, adrenal and testis⁵ (https://www.proteinatlas.org). Reminiscent of the amyloid precursor protein APP, TMEM106B is sequentially processed through ectodomain shedding, followed by intramembrane proteolysis, with possible variability in the intramembrane cleavage site. Lysosomal proteases have been implicated in the cleavage of TMEM106B in the C-terminal luminal domain, but no specific enzymes have been identified. Although the cleavage site is unknown, it has been shown indirectly to be at a position close to G127. The resulting C-terminal fragment contains five glycosylation sites at N145, N151, N164, N183 and N256. Following shedding of the ectodomain, the N-terminal fragment is cleaved by signal peptide peptidase-like 2a (SPPL2a), possibly at two different sites around residue 106 (ref.⁶).

Genetic variation at the TMEM106B locus has been identified as a risk factor for frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), especially for individuals with granulin (GRN) gene mutations⁷. The change of T185 to serine (encoded by rs3173615) has been suggested to protect against FTLD-TDP (ref.⁸), possibly because the protein with a serine is more rapidly degraded⁹. In addition, the protective effects of the noncoding variant rs1990622 have been attributed to reduced expression of TMEM106B (refs.^3,8). Levels of TMEM106B are elevated in FTLD-TDP (ref.¹⁰). TMEM106B has also been reported to be involved in other diseases^3,4. Genome-wide association studies have also implicated TMEM106B in age-associated phenotypes in the cerebral cortex¹¹. Furthermore, the variant rs1990622 has been reported to correlate with reduced neuronal degeneration during ageing, independently of disease^11,12.

Previously, cryogenic electron microscopy (cryo-EM) imaging allowed atomic structure determination of filaments of the proteins tau^13–17, α-synuclein¹⁸, amyloid-β (Aβ)^19,20 and TDP-43 (ref.²¹) that were extracted from the brains of individuals with different neurodegenerative diseases. Cryo-EM structures revealed that distinct folds characterize different diseases. For tauopathies, this has made it possible to classify known diseases further and to identify new disease entities¹⁷.

Cryo-EM structure determination can also be used to identify previously unknown filaments. Here we have used cryo-EM to show that residues 120–254 from the luminal domain of TMEM106B form amyloid filaments in human brains. We initially observed TMEM106B filaments in the brains of individuals with familial and sporadic tauopathies, Aβ amyloidoses, synucleinopathies and TDP-43 proteinopathies. However, the role of TMEM106B filaments in disease remains unclear. They were not observed in brains from young individuals, but their presence in brains from older individuals with normal neurology (controls) indicates that TMEM106B filaments may form in an age-dependent manner. It remains to be determined how these findings relate to those from genetic association studies.

Using sarkosyl extraction protocols that were originally developed for α-synuclein^18,22, we observed a common type of filament that seemed to lack a fuzzy coat in the cryo-EM micrographs from cases of various conditions with abundant filamentous amyloid deposits. Structure determination to resolutions sufficient for de novo atomic modelling revealed that the ordered cores of these filaments consisted of residues 120–254 from the carboxy-terminal, luminal domain of TMEM106B and that the filaments were polymorphic (Fig. ​(Fig.1).1). We solved the structures of TMEM106B filaments from a number of brain regions of 22 individuals with abundant amyloid deposits, and from the frontal cortex of 3 individuals with normal neurology and no or only a few amyloid deposits (cases 1–25; Methods, Table ​Table11 and Extended Data Table ​Table1).1). The neurodegenerative conditions for which we solved structures of associated TMEM106B filaments included sporadic and inherited Alzheimer’s disease, pathological ageing, corticobasal degeneration, sporadic and inherited FTLD (FTLD-TDP types A and C, and familial frontotemporal dementia and parkinsonism linked to chromosome 17 caused by MAPT mutations), argyrophilic grain disease, limbic-predominant neuronal inclusion body four-repeat tauopathy, ageing-related tau astrogliopathy, sporadic and inherited Parkinson’s disease, dementia with Lewy bodies, multiple system atrophy (MSA) and amyotrophic lateral sclerosis. We observed three different TMEM106B protofilament folds (I–III; Fig. ​Fig.11 and Extended Data Figs. ​Figs.11–4). Filaments with fold I were more common than filaments with folds II or III. For all three folds, we determined the structures of filaments that were made of a single protofilament. We also determined the structures of filaments comprising two protofilaments of fold I, related by C₂ symmetry. In each individual, we observed only filaments with a single fold, without a clear relationship between folds and diseases.

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Fig. 1

Three TMEM106B protofilament folds from human brains.

a, Amino acid sequence of TMEM106B, with residues that form β-strands in folds I, IIa, IIb and III indicated with arrows. Residue 185 is either threonine or serine. b–d, Cryo-EM density maps (in transparent grey) and atomic models for TMEM106B protofilament folds I (case 1, b), II (case 19, c) and III (case 17, d). Two alternative conformations of fold II (IIa and IIb) are indicated within dashed boxes. Residues 120–166 are shown in yellow; residues 167–210 in light blue and residues 211–254 in magenta.

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Extended Data Fig. 1

TMEM106B filament reconstructions.

Cross-sections of TMEM106B filaments, perpendicular to the helical axis and with a projected thickness of approximately one β-rung, for all cases examined. Orange arrows point at additional densities in front of Y209; magenta arrows point at additional densities in front of K178. Scale bar, 5nm.

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Extended Data Fig. 4

Close-up views of cryo-EM densities.

a. Cryo-EM densities (transparent grey) for N-linked glycosylation of asparagines 145, 151, 164 and 183 in fold III, showing the first, most ordered glcNac saccharide of the glycan chains. b. Density for residues 187–192 in fold I (left, orange), fold II (middle, blue) and fold III (right, pink), as viewed from the top (top panels) and the side (bottom panels). Carbonyl oxygens of P189 are indicated with black arrows. In folds I and II, P189 adopts a trans-configuration, whereas in fold III, P189 adopts a cis-conformation. c. Density for the N-terminal S120 residue, and its surrounding residues E161, H239, E241. The latter are one β-rung above (i+1) the β-rung of S120 (i) in folds I and II. In fold III, H239 and E241 are two β-rungs above (i+2) the β-rung of S120.

Extended Data Table 1

Further details on cases

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Further details on cases

AD: sporadic Alzheimer’s disease; FAD: familial Alzheimer’s disease; EOAD: sporadic early-onset Alzheimer’s disease; PA: pathological aging; CBD: corticobasal degeneration; FTDP-17T: familial frontotemporal dementia and parkinsonism linked to chromosome 17 caused by MAPT mutations; AGD: argyrophilic grain disease; LNT: limbic-predominant neuronal inclusion body 4R tauopathy; ARTAG: aging-related tau astrogliopathy; PD: sporadic Parkinson’s disease; PDD: sporadic Parkinson’s disease dementia; FPD: familial Parkinson’s disease; DLB: dementia with Lewy bodies; MSA: multiple system atrophy; FTLD-TDP-A: familial frontotemporal lobar degeneration with TDP-43 inclusions type A; FTLD-TDP-C: sporadic frontotemporal lobar degeneration with TDP-43 inclusions type C; ALS: amyotrophic lateral sclerosis; Control: neurologically normal individual. FL: frontal lobe; TL: temporal lobe; NAcc: nucleus accumbens; HPC: hippocampus; CG: cingulate gyrus; AMG: amygdala; PU: putamen; MC: motor cortex.

The TMEM106B folds shared a similar five-layered ordered core comprising residues S120–G254 and contained 17 β-strands, each ranging between 3 and 15 residues. Our best maps for filaments with folds I, II and III had resolutions of 2.6, 3.4 and 2.8Å, and came from case 1 (sporadic Alzheimer’s disease), case 19 (MSA) and case 17 (MSA), respectively (Fig. ​(Fig.1).1). TMEM106B remained fully glycosylated in all folds, as reflected by large extra densities corresponding to glycan chains attached to the side chains of N145, N151, N164 and N183. The fifth glycosylation site at N256 is outside the ordered core, with the C-terminal 20 residues being probably disordered. We divide the sequence that forms the ordered cores of the folds into three regions according to their degree of structural conservation: the amino-terminal region (S120–T166) is conserved in all three folds; the C-terminal region (Y211–G254) is conserved only in folds I and II; and the middle region (A167–M210) varies between folds.

The N-terminal region, S120–T166, forms the first two layers of the five-layered ordered cores. It comprises one long and five short β-strands that constitute a tightly packed core with hydrophobic and neutral polar residues on one side, and a large polar cavity that is filled by solvent on the other side. The three glycosylation sites in this region are located in the outer layer, adopting an extended conformation. The N-terminal residue S120 in the inner layer is buried inside the ordered core, where it packs closely against E161 from the N-terminal region and H239 and E241 from the C-terminal region (Extended Data Fig. ​Fig.44).

The C-terminal region, Y211–G254, forms the two central layers of the ordered cores. It adopts a compact hairpin-like structure, the ends of which are held together by a disulfide bond between C214 and C253. Segment F237–E246 that packs against the N-terminal region has the same conformation in all three folds, whereas in the rest of the hairpin-like structure, 15 residues have opposite ‘inward/outward’ orientations in fold III compared with those in folds I and II. Moreover, despite similar interfaces between N- and C-terminal parts in all three folds, these regions in fold III are separated along the filament axis by one more rung than in folds I and II (Extended Data Fig. ​Fig.3e3e).

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Extended Data Fig. 3

Comparisons of TMEM106B folds I-III.

a Ribbon view of folds I-III aligned at residues 120–166 (centre) with close-up views for three regions (b-d). e. Cartoon views for three subsequent β-rungs for each fold, viewed from the left-hand side of the ribbon view in panel A. Fold I is shown in orange; fold IIa in blue; fold IIb in green; fold III in pink. Schematics of fold I (f), fold II (g), and fold III (h). Negatively charged residues are shown in red, positively charged residues in blue, polar residues in green, apolar residues in white, sulfur-containing residues in yellow, prolines in purple, and glycines in pink. Thick connecting lines with arrowheads indicate β-strands.

The middle region, A167–M210, forms the fifth layer of the ordered cores and contains the fourth glycosylation site at N183. In fold I, this region packs loosely against the other side of the C-terminal hairpin-like region with the formation of three large amphipathic cavities. In fold II, these internal cavities are smaller than in fold I. We observed two subtypes of fold II (IIa and IIb) that differed mainly by the conformation of segment A167–I187. The packing of the middle region against the C-terminal region is tightest in fold III, leaving only one sizable cavity with a salt bridge between E206 and K220. Only fold III shows cis isomerization of P189. In folds IIb and III, there is a large extra density at the end of the side chain of K178, suggesting that this residue may be post-translationally modified. Likewise, there is an extra density in front of the side chain of Y209 in fold I, but not in the other folds (Extended Data Fig. ​Fig.1).1). It is possible that these residues determine the formation of the different folds. Genotyping of all individuals (Table ​(Table1)1) showed that the alleles encoding T185 or S185 were equally represented. Individuals with fold I were homozygous for T185 or S185, or heterozygous, indicating that fold I can accommodate a threonine or a serine at position 185. Owing to the compatibility of both residues with the glycosylation motif at N183, no differences in the associated glycan densities were observed. Fold II was found only in case 19, which was homozygous for T185. Seven out of eight individuals with fold III were homozygous for S185, with the remaining individual being heterozygous. It is possible that the packing of the side chain of residue 185 in the interior of fold III leaves insufficient space to accommodate a threonine.

In all three folds, residues G177–N183 adopt a conserved conformation, with the positively charged residues K178 and R180 pointing outwards. In filaments made of two protofilaments with fold I, two pairs of these residues are on opposite sides of a contiguous extra density that runs along the helical symmetry axis. As the cofactor responsible for this density probably does not obey the imposed helical symmetry, the map in this region is of insufficient quality to allow its identification. Although we did not solve the structures of filaments comprising two protofilaments of folds II or III, the micrographs of case 19, the only individual for which we observed filaments with fold IIa/b, and the micrographs of case 21, with fold III, also contained wider filaments that probably comprised two TMEM106B protofilaments (Extended Data Fig. ​Fig.55).

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Extended Data Fig. 5

TMEM106B filaments comprising two protofilaments.

a. Cryo-EM micrographs with filaments comprising two protofilaments, with fold I for MSA case 18 (I-d; left), with putative fold II for MSA case 19 (II-d; middle), and with putative fold III for FTLD-TDP-C case 21 (III-d; right); α-synuclein filaments typical for MSA are also indicated (MSA). b. Cryo-EM density map and atomic model of TMEM106B filaments comprising two protofilaments of fold I. c. Three orthogional close-up views of the inter-protofilament interface.

In the absence of an experimentally determined native structure, we examined the structure of TMEM106B as predicted by AlphaFold²³ (Extended Data Fig. ​Fig.6).6). Whereas the formation of amyloid filaments is often associated with natively unfolded proteins or low-complexity protein domains, the sequence S120–G254, which spans the ordered core of TMEM106B filaments, is confidently predicted to be a globular domain of the immunoglobulin-like β-sandwich fold. Glycosylation sites at N145, N151, N164 and N183 are positioned on the outside of the fold, and the disulfide bond between C214 and C253 is also predicted to form in the native structure. The β-sandwich domain is connected to a single transmembrane helix, without a flexible linker sequence. Moreover, there is a hydrophobic surface patch at this end of the domain, suggesting that it is positioned close to the membrane. It thus seems unlikely that the cleavage site at S120, the buried N-terminal residue in all TMEM106B filaments, can be accessed by lysosomal proteases. Shedding of the luminal domain may happen in a noncanonical way.

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Extended Data Fig. 6

AlphaFold prediction of TMEM106B.

a. Amino acid sequence of TMEM106B. Predicted α-helices are represented with wavy blue lines; predicted β-strands with red arrows. Residues 1–90, 91–119, 120–166, 167–210, 211–254 and 255–274 are coloured in grey, green, yellow, light blue, magenta and dark blue, respectively. b. AlphaFold prediction of TMEM106B. c. Close-up view of the AlphaFold prediction of part of the transmembrane helix (green) and the lumnal domain, with glycosylation sites N145, N151, N164, N183 and disulfide bridge C214, C253 shown as sticks. d. Hydrophobicity surface view at the interface between the lumenal domain and the transmembrane helix. Residues 119–121 are shown as sticks. e. Two orthogonal close-up views of residues close to the lysosomal membrane surface.

We previously showed that distinct amyloid folds of tau, α-synuclein, Aβ and TDP-43 characterize different neurodegenerative diseases^{13–18,20,21}. We now describe the presence of TMEM106B filaments in many of these diseases, without a correlation between folds and diseases. Therefore, we also examined 16 brains from individuals with normal neurology that varied in age between 20 and 101 years. By immunoblotting with an antibody raised to a peptide corresponding to residues 239–250 of human TMEM106B (antibody TMEM239), the sarkosyl-insoluble fractions from disease cases showed a band of 29kDa, which probably corresponded to the 17-kDa C-terminal fragment plus 12kDa of glycosylation and other modifications (Fig. ​(Fig.22 and Extended Data Fig. ​Fig.7).7). This band was not present in the brains from individuals with normal neurology aged less than 46 years, excluding the possibility that TMEM106B assembly was an artefact caused by tissue extraction. However, we consistently observed the 29-kDa band in the brains from control individuals older than 69 years. Interestingly, the 29-kDa band was not present in the frontal cortex from a 15-year-old individual with early-onset dementia with Lewy bodies²⁴ (Fig. ​(Fig.2b).2b). In agreement with these observations, immunohistochemistry of brain sections with the antibody TMEM239 showed staining of inclusions in disease cases and older control individuals, but not in younger controls (Fig. ​(Fig.33 and Extended Data Fig. ​Fig.8).8). It is not known how these inclusions relate to lysosomes. Cryo-EM structure determination showed the presence of TMEM106B filaments with one or two protofilaments of fold I in the frontal cortex from three controls, aged 75, 84 and 101years.

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Fig. 2

Immunoblotting of TMEM106B inclusions from human brains.

a, Analysis with anti-TMEM239 antibody (residues 239–250) of sarkosyl-insoluble extracts from the frontal cortex of 16 neurologically normal individuals aged 20–101 years. Cryo-EM structures of TMEM106B filaments were determined from the frontal cortex of individuals aged 75, 84 and 101 years. b, Analysis with anti-TMEM239 antibody of sarkosyl-insoluble extracts from frontal or temporal cortex of 7 individuals with abundant filamentous amyloid deposits made of various proteins. For source images for the gels, see Supplementary Fig. 1.

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Fig. 3

Immunostaining of TMEM106B inclusions in human brain sections.

a, b, Analysis with anti-TMEM239 (residues 239–250) of frontal cortex from a 25-year-old (a) and an 84-year-old (b) individual with normal neurology. No specific staining was observed in a, but abundant globular cytoplasmic inclusions and stained brain cell processes were present in b. c–e, Higher magnifications of inclusions from b. Nuclei were counterstained in red. Scale bars, 50µm (a, b) and 20µm (c–e).

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Extended Data Fig. 7

Immunoblot analysis of TMEM106B expressed in E. coli establishes the specificity of antibody TMEM239.

a. Diagram of the TMEM106B sequence, coloured in accordance with Fig. ​Fig.1,1, with the immunogen of antibody TMEM239 (residues 239–250) indicated. b. Coomassie blue-stained gel and immunoblot (antibody TMEM239) of recombinant C-terminal TMEM106B fragment (WT; residues 120–274) and the immunogen-deletion construct (Δ239-250). Pellets from 1ml cell extracts and TMEM106B purified from inclusion bodies (see Methods) were used. Red arrows indicate TMEM106B bands; red asterisks indicate non-specific binding.

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Extended Data Fig. 8

TMEM106B immunohistochemistry.

Immunostaining of sections from the frontal cortex of neurologically normal individuals aged 24–82 years (yo: year-old) (a-i; m-o) and individuals with abundant filamentous amyloid deposits made of various proteins (j-l). a-l. Sections were stained with C-terminal anti-TMEM239 antibody. m-o. Sections were stained with an N-terminal anti-TMEM106B antibody (Bethyl Labs). Nuclei were counterstained in red. Scale bar, 50µm (a-o). TMEM106B inclusions were visualised with the C-terminal antibody, while the N-terminal antibody showed only diffuse cytoplasmic staining. Previous studies also reported diffuse cytoplasmic staining with N-terminal TMEM106B antibodies^29,41. Staining with the C-terminal antibody showed age-dependent assembly of TMEM106B, with no inclusions in the frontal cortex of young individuals (a-d, and Fig. ​Fig.3a),3a), a small number in middle-aged individuals (e, f) and abundant inclusions in older individuals (g-i and Fig. 3b–e). Inclusions of TMEM106B were also present in cases with neurodegenerative diseases who were older than 59 years. By immunoblotting with antibody TMEM239, a 29 kDa band was present in cases with inclusions.

Our results suggest that amyloid filaments of the lysosomal protein TMEM106B form in an age-dependent manner in human brains, without a clear mechanistic connection to disease. Until now, the presence of abundant intraneuronal amyloid filaments in human tissues has always been associated with disease. Dominantly inherited mutations in the genes encoding tau, α-synuclein and TDP-43 cause neurodegenerative diseases. In addition, cryo-EM structures of amyloid filaments made of these proteins exhibit distinct folds that are characteristic of different diseases^13–18,21. Although TMEM106B has been associated with frontotemporal dementias and other diseases, the evidence for a causal relationship between TMEM106B aggregation and disease remains unclear, and distinct TMEM106B folds do not characterize different diseases. Instead, our observations suggest that TMEM106B filaments form in an age-dependent manner. Like lipofuscin, a lysosomal complex of oxidized proteins and lipids that develops in an age-dependent manner in many tissues²⁵, TMEM106B filaments may also form in lysosomes, even though staining for TMEM106B inclusions was not always associated with the presence of lipofuscin autofluorescence. Lysosomal dysfunction has been implicated in the pathogenesis of neurodegenerative diseases²⁶. Further studies are needed to determine whether TMEM106B filaments can be found in tissues other than the central nervous system and to assess the role of filament formation in relation to human ageing and pathologies.

Methods

Helical reconstruction

Movie frames were gain corrected, aligned, dose weighted and then summed into a single micrograph using RELION’s own motion correction program³¹. The micrographs were used to estimate the contrast transfer function (CTF) using CTFFIND-4.1 (ref.³²). All subsequent image-processing steps were performed using helical reconstruction methods in RELION (refs.^33,34). TMEM106B filaments were picked manually, as they could be distinguished from filaments made of tau, Aβ, α-synuclein and TDP-43 by their general appearance and the apparent lack of a fuzzy coat. TMEM106B filaments comprising one or two protofilaments were picked separately. For all datasets, reference-free 2D classification was performed to select suitable segments for further processing. Initial 3D reference models were generated de novo from the 2D class averages using an estimated rise of 4.75Å and helical twists according to the observed crossover distances of the filaments in the micrographs³¹ for datasets of cases 10 (LNT; folds I-s and I-d), 18 (MSA; fold I-d), 19 (MSA; folds IIa and IIb) and 17 (MSA; fold III). Refined models from these cases, low-pass filtered to 10–20Å, were used as initial models for the remaining cases. Combinations of 3D auto-refinements and 3D classifications were used to select the best segments for each structure. For all datasets, Bayesian polishing³⁵ and CTF refinement³⁶ were performed to further increase the resolution of the reconstructions. Final reconstructions were sharpened using the standard post-processing procedures in RELION, and overall final resolutions were estimated from Fourier shell correlations at 0.143 between the two independently refined half-maps, using phase randomization to correct for convolution effects of a generous, soft-edged solvent mask³⁷. Further details of data acquisition and processing for the datasets that resulted in the best maps for five different TMEM106B filaments (filaments made of one or two protofilaments with fold I, as well as filaments made of one protofilament with fold IIa, fold IIb or fold III) are given in Extended Data Table ​Table22.

Extended Data Table 2

Cryo-EM data acquisition and structure determination

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Cryo-EM data acquisition and structure determination

Online content

Any methods, additional references, Nature Research reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10.1038/s41586-022-04650-z.

Acknowledgements

Author contributions

D.A., M.B., M. Huang, S.L., Y. Shi and Y.Y. are listed in alphabetical order. K.L.N., S.M., M.M., Y.Saito, M.Y., K.H., T.L., T.R., G.G.K., J.v.S., M.T., M. Hasegawa., B.G., B.R.-F. and M.G. identified patients and performed neuropathology; M.S., Y.Shi, M. Huang., D.A., Y.Y., W.Z., H.J.G., R.V., G.I.H., A.T. and M. Hasegawa. performed brain sample analysis; M.S., Y.Shi, D.A., Y.Y., W.Z. and A.K. collected cryo-EM data; M.S., Y.Shi, D.A., Y.Y., S.L., W.Z., B.R.-F., A.G.M. and S.H.W.S. analysed cryo-EM data; M.S. and M. Huang. performed immunoblot analysis; S.L. performed recombinant protein expression and epitope mapping; M.B. and M.G.S. performed immunohistochemistry. M.G. and S.H.W.S. supervised the project. All authors contributed to the writing of the manuscript.

Peer review

Data availability

Cryo-EM maps have been deposited in the Electron Microscopy Data Bank (EMDB) under accession numbers 14174 for I-s of case 1, 14176 for I-d of case 18, 14187 for IIa-s and 14188 for IIb-s of case 19, and 14189 for III-s of case 17. Corresponding refined atomic models have been deposited in the Protein Data Bank under accession numbers 7QVC for I-s of case 1, 7QVF for I-d of case 18, 7QWG for IIa-s and 7QWL for IIb-s of case 19, and 7QWM for III-s of case 17.

Competing interests

The authors declare no competing interests.

Footnotes

Contributor Information

Michel Goedert, Email: ku.ca.mac.bml-crm@gm.

Sjors H. W. Scheres, Email: ku.ca.mac.bml-crm@serehcs.

References