Isolation of human brain derived PHF
Tau paired-helical filaments (PHF) were isolated from post-mortem frontal cortex tissue of an Alzheimer's disease (A.D.) patient (purchased from Tissue Solution). The enrichment procedure was modified from Jicha et al, 1997 and Rostagno and Ghiso, 2009. Briefly, approximately 15 g of frontal cortex tissue were thawed on ice and homogenized using a glass Dounce homogenizer in 50 mL of a homogenization buffer consisting of 0.75 M NaCl, 100 mM (MES) pH 6.8, 1 mM EGTA, 0.5 mM MgSO4, 2 mM DTT, and protease inhibitors (Complete; Roche 11697498001). The homogenate was then incubated at 4°C for 20 min for microtubule depolymerization, before being transferred into polycarbonate centrifuge bottles (16 x 76 mm; Beckman 355603) and centrifuged at 11,000 g (12,700 RPM) in an ultracentrifuge (Beckman, XL100K) for 20 min at 4°C using the pre-cooled 70.1 rotor (Beckman, 342184). Pellets were kept on ice. Supernatants were pooled into polycarbonate bottles and centrifuged again at 100,000 g (38,000 RPM) for 1 h at 4°C in the 70.1 Ti rotor to isolate PHF-rich pellets, whereas soluble tau remained in the supernatants. The pellets from the first and second centrifugations were resuspended in 120 mL of extraction buffer [10 mM Tris-HCl pH 7.4, 10% sucrose, 0.85 M NaCl, 1% protease inhibitor (Calbiochem 539131), 1 mM EGTA, 1% phosphatase inhibitor (Sigma P5726 and P0044)]. The solution was then transferred into polycarbonate centrifuge bottles (16 x 76 mm; Beckman 355603) and centrifuged at 15,000 g (14,800 RPM) in an ultracentrifuge (Beckman, XL100K) for 20 min at 4°C using the 70.1 Ti rotor. In the presence of 10% sucrose and at low-speed centrifugation, most PHF remained in the supernatant whereas intact or fragmented NFTs and larger PHF aggregates were pelleted. The pellets were discarded. 30% Sarkosyl (Sigma L7414-10ML) was added to the supernatants to a final concentration of 1% and stirred at R.T. for 1 h. This solution was then centrifuged in polycarbonate bottles at 100,000 g (38,000 RPM) for 1 h at 4°C in the 70.1 Ti rotor, and the pellets containing PHF-rich material were resuspended in 50ul PBS/ 1g of brain tissue. The resuspended PHF was then sonicated on ice for 60s with 1s-on/1s-off cycles at 20% amplitude. Aliquots were snap frozen and stored at -80°C.
Preparation of Tau aggregates
Tau PHF isolated from Human A.D. brain was used as seed to induce the templated aggregation of human full length 2N4R Tau monomers (35uM, Biotechne in a 72h incubation at 37C on a shaker at 1000 rpm. These aggregates were stored at -20°C. Three days before the treatment of neurons, these aggregates were thawed and used as seeds (1:200) in a secondary aggregation reaction in the presence of 10 µM tau monomers (72h at 37C, 1000 rpm).
Lentiviral vector production and infection
The L.V.s were pseudotyped as vesicular stomatitis virus glycoprotein G (VSV-G). LV-PGK-MitoTimer and LV-PGK-MitoGoTeam2 (G1B3 promoter instead of PGK for astrocytes) were produced by transfection of human embryonic kidney (HEK) 293T cells (mycoplasma-negative, ATCC, LGC Standards GmbH, Germany). L.V.s were concentrated by ultracentrifugation and resuspended in phosphate-buffered saline (dPBS, Gibco, Life Technologies, Zug, Switzerland) supplemented with 1% bovine serum albumin (BSA, Sigma‒Aldrich, Buchs, Switzerland). The viral particle content in each batch was determined using a p24 antigen enzyme-linked immunosorbent assay (p24 ELISA, RETROtek; Kampenhout, Belgium). The stocks were stored at − 80°C until use and diluted to 100,000 ng/ml in PBS/1% BSA. For neuronal expression of mitochondrial biosensors, cells were infected at DIV 5 with lentiviral vectors (L.V.s) expressing reporter genes, mainly in neurons. The LV-PGK vectors used in this study have been previously described by Schwab and colleagues [10]. The reporter gene contained a woodchuck hepatitis virus B postregulatory element (WPRE) and the mouse PGK promoter. Astrocytes were infected at 8 DIV with lentiviral vectors (LV) expressing the mitochondrial reporter gene. The gfaABC1D promoter was ligated to enhancer B(3) to generate the G1B3 promoter, which was subsequently cloned and inserted into the SIN-cPPT-gateway-WPRE-miR124T transfer plasmid, which contains four copies of the neuron-specific miRNA-124 target sequence (miR124T; full homology) to repress transgene expression in neurons, WPRE and the central polypurin tract (cPPT) to increase transgene expression and a 400-nucleotide deletion in the long 3′ terminal repeat (self-inactivating vector) to increase biosafety.
2D Primary pure neuron culture
Rat primary cortical cultures were prepared from Sprague-Dawley rats (Charles River Laboratories L'Arbresle, France) at postnatal day 1. The neocortex and hippocampus were isolated by removing the dura, brainstem, olfactory bulbs and subcortical regions. Isolated cortex and hippocampus were cut into small pieces and dissociated by enzymatic digestion for 30 minutes at 37°C in dissociation buffer (papaine, CaCl2, EDTA, and HEPES; all from Invitrogen, Carlsbad, CA, USA). DNase (Invitrogen, Basel, Switzerland) was added, and the mix was incubated for another 30 min at 37C. After mechanical dissociation consisting in pipetting the tissue up and down, the cell suspension was passed through a cell strainer and dispersed cells were plated onto 96-well tissue culture plates coated with poly-D-Lysine (Corning, 3841) at 30K cells/well. Cells were plated in Neurobasal medium (Invitrogen, Basel, Switzerland) without phenol red, with the addition of L-glutamine (2 mM; Sigma, Buchs, Switzerland), 10% FCS (Invitrogen, Basel, Switzerland), and penicillin/streptomycin (Sigma, Buchs, Switzerland) and incubated at 37C in the presence of 5% CO2. 1.5 hours after plating the cells, the medium was replaced with Neurobasal medium containing 2mM L-Glutamine, B-27TM (Gibco, 17504-044), and penicillin/streptomycin. After 4 days in culture, cell proliferation was blocked by treatment with 2.5 µM cytosine arabinoside (Invitrogen, Basel, Switzerland).
3D Primary neuron-glial cultures
For 3D culture, hippocampus of E17 Wistar rat embryos was dissected, and the cells were dissociated with a neuronal dissociation kit (130-092-628). Mixed cells were plated at a density of 30K cells/cm2 in 24-well or 96-well glass-bottom plates (Ibidi 82426, Corning™ 356234) coated with Matrigel in 200 µM DMEM (Gibco 41965-039, 25 mM glucose) supplemented with 0.25% L-glutamine (Gibco, 25030081), 1% penicillin/streptomycin (Thermo Fisher Scientific 15140-122) and 2% B27 (17504044, Gibco) and incubated at 37°C and 5% CO2.
Immunofluorescent stainings
Three days after treatment, cells were fixed with 4% PFA (Sigma, 158127-500G) for 15 min at 37°C and stored in PBS at 4°C for further analysis. All the incubations and extractions were carried out in PBST (10010-015, Gibco), 0.3% Triton X-100 (Sigma–Aldrich, X100-100ML), and 3% NHS (Gibco, 16050-122). Primary antibody incubation was performed overnight with rabbit anti-VGlut1 (Cell Signaling Technology, 1230.31; 1:500), chicken anti MAP2 (Abcam, ab5392, 1:1'000), goat anti-PSD95 (Abcam, ab12093; 1:500), or mouse anti-NeuN (Chemicon, MAB337) and anti-GFAP (Dako, GA52461-2) antibodies. Secondary antibody incubation was conducted for 60 min at room temperature with Alexa Fluor 488-, 555- or 647-conjugated highly cross-adsorbed donkey anti-goat, donkey anti-rabbit or donkey anti-chicken antibodies, respectively (1:500; Invitrogen A31573, Invitrogen A11055, Jackson IR 703-545-155). After additional incubation in DAPI (Merck, 268298; 1:5,000), the cells were stored at 4°C in PBS.
Microscopy and image acquisition
In this study, 2D cultures (Fig. 1) and live imaging (Fig. 4–5) were acquired with an inverted microscope (Nikon Eclipse Ti-2) equipped with an Okolab cage incubator (H201-T-UNIT), the Perfect Focus System (PFS), CFI Plan Apochromat Lambda D 40X and 60X Oil, and Lumencor SPECTRA X Light Engine. 3D culture (Fig. 2) were acquired with fully motorized model Ni-E equipped with spinning-disk confocal technology (CrestOptic, X-Light V3) and CFI Plan Apochromat Lambda D 40X and 60X Oil. All images were acquired with Nikon's software suite NIS HC v.5.42.
Images analysis
Images were analyzed using Nikon NIS AI or H.C. v.5.42 and the General analysis 3 (GA3) module of this software. For 2D culture analysis, 8000x8000 pixels mosaic images of each well were analyzed to quantify the number of DAPI-labeled cells and neuritic segments, using MAP2 labeling reconstruction. MAP2 was segmented and skeletonized to measure total branch length. MAP2 in the vicinity of DAPI + nuclei was excluded by subtraction of dilated the DAPI objects.
For synapse analysis all images were enhanced AI-denoising tool. VGlut1 + and PSD-95 + labeled puncta were quantified in regions of interest free of cell nuclei. Synaptic markers were analyzed using a spot detection algorithm. Overlay points between spots were quantified to detect vGlut1/PSD-95 active areas. All data were normalized by the MAP2 area per ROI. The GA3 analysis script used is accessible in the supplementary material. For the analysis of 3D cultures, confocal acquisitions at 60X were performed on approximately 30 focal sections of 0.3 µm of 2048x2048 pixels. Between 5 and 10 volumes of interest located in proximal neurites emanating from neurospheroids were selected to quantify vGlut1 and PSD95 in three dimensions. Volumes corresponding to PSD95 were used to create three-dimensional objects, while a spot detection algorithm was used to identify vGlut1 puncta. To include only vGlut1 volumes in contact with PSD-95, the PSD95 volume was dilated by 0.1 µm. The sum of the volumes of vGlut1 spots in the dilated volume of PSD95 (PSD-95 shell) was then calculated. All GA3 analysis scripts are available in the data repository.
Mitochondrial live monitoring of morphology and turnover was conducted as previously described [8, 9] at 40x magnification. We acquired images before treatment as a baseline (B.L) and then every 2 h for 3 days. Live Mitotimer analysis was conducted within a small ROI placed on distal cell processes to ensure the selection of cellular endpoints. A minimum of 12 processes were analyzed for each image sequence. Briefly, Total mitotimer was obtained from the two fluorescent channels and used for segmentation. Only individual and well reconstructed mitochondria were considered for measurements of morphology and fluorescence intensity values (Red and Green intensities, red/green ratio, elongation, area, length, skeleton branches, junctions, circularity, diameter, surface, shape factor, and mitochondria number). Finally, after log transformation and averaging by frame, a score was calculated a the fold-change relatively to the first frame (B.L). To analyze mitochondrial ATP levels in neurons with neuronal Go-ATeam2 [11] expression, single mitochondrial units were semi manually segmented into 12 axons per replicate to conduct ratio measurements. The measurements were further processed like Mitotimer.
Synaptosome extraction
The cells were rinsed several times, collected, and snap-frozen. Homogenization was performed on ice in PBS. The samples were centrifuged at 1300 × g for 3 min at 4˚ C to pull down the membrane fragments, nuclei, and cells. The supernatant was coupled with Anti-tomm22 micro-Beats (30min at 4˚ C) to remove free mitochondria through Magnetic-assisted cell sorting (MACS) (Miltenyi Biotec, 130-096-946, 130-042-401). The mitochondria-depleted flow-through was centrifuged at 13,000 × g for 10 min at 4˚ C to pellet synaptosomes (100ul of PBS resuspension, stored frozen until further analysis).
Synaptosomes proteomic mass spectrometry
(1) Protein digestion: Synaptosomal fractions were digested according to a modified version of the iST method 80 (named miST method). Briefly, 50 µl solution of PBS was supplemented with 50 µl miST lysis buffer (1% sodium deoxycholate, 100 mM Tris pH 8.6, 10 mM DTT) and heated at 95°C for 5 min. Samples were then diluted 1:1 (v:v) with water, and reduced disulfides were alkylated by adding ¼ vol of 160 mM chloroacetamide (final 32 mM) and incubating at 25°C for 45 min in the dark. Samples were adjusted to 3 mM EDTA and digested with 0.5 µg Trypsin/LysC mix (Promega #V5073) for 1h at 37°C, followed by a second 1h digestion with a second and identical aliquot of proteases. To remove sodium deoxycholate and desalt peptides, two sample volumes of isopropanol containing 1% TFA were added to the digests, and the samples were desalted on a strong cation exchange (SCX) plate (Oasis MCX; Waters Corp., Milford, MA, USA) by centrifugation. After washing with isopropanol/1%TFA, peptides were eluted in 250 µl of 80% MeCN, 19% water, and 1% (v/v) ammonia; (2) Liquid chromatography-tandem mass spectrometry: Eluates after SCX desalting were frozen, dried, and resuspended in variable volumes of 0.05% trifluoroacetic acid and 2% acetonitrile to equilibrate concentrations. Approximately 1 µg of each sample was injected into the column for nanoLC-MS analysis. (3) M.S. and M.S. data analysis: Dependent LC-MS/MS analysis of the TMT sample was performed on a Fusion Tribrid Orbitrap mass spectrometer (Thermo Fisher Scientific) interfaced through a nano-electrospray ion source to an Ultimate 3000 RSLCnano HPLC system (Dionex). Peptides were separated on a reversed-phase custom-packed 40 cm C18 column (75 µm ID, 100 Å, Reprosil Pur 1.9 µm particles, Dr. Maisch, Germany) with a 4–76% acetonitrile gradient in 0.1% formic acid (total time 140 min). Full MS survey scans were performed at 120'000 resolution. A data-dependent acquisition method controlled by the Xcalibur 4.2 software (Thermo Fisher Scientific) was used to optimize the number of precursors selected ("top speed") of charge 2 + to 5 + while maintaining a fixed scan cycle of 1.5s. The precursor isolation window used was 0.7 Th. Full survey scans were performed at a 120'000 resolution, and a top speed precursor selection strategy was applied to maximize acquisition of peptide tandem M.S. spectra with a maximum cycle time of 0.6s. HCD fragmentation mode was used at a normalized collision energy of 32% with a precursor isolation window of 1.6 m/z, andthe MS/MS spectra were acquired in the ion trap. The peptides selected for MS/MS were excluded from further fragmentation for 60s. Tandem MS data were processed using MaxQuant software (version 1.6.3.4) 81 incorporating the Andromeda search engine 82. UniProt reference proteome (RefProt) databases for Homo sapiens and mice were used, supplemented with sequences of common contaminants. Trypsin (cleavage at K, R) was used as the enzyme definition, allowing for two missed cleavages. The carbamidomethylation of cysteine was specified as a fixed modification. N-terminal acetylation of proteins and oxidation of methionine are specified as variable modifications.
Proteomic data analysis
MaxQuant data were further processed using the Perseus software[12] and Microsoft Excel. We used a cutoff for the presence of a protein in a sample such as Razor Peptide Score > 2 and MS/MS Count > 2; 29% of the proteins were discarded in this process. IBAQ values are the sum of the intensities of all unique peptides for a protein divided by the number of theoretical tryptic peptides between six and 30 amino acids in length[17]. LFQ were calculated according to the number of unique peptides of a protein on the total number of peptides. The relative protein abundance was calculated as the sum of the relative intensity-based absolute quantification (rIBAQ) of all selected proteins that were independently present in each replicate. Protein Annotation was conducted in Perseus using the Gene Ontology databases (Biological Process (B.P.), Cellular Compartment (CC), Molecular Function (M.F.)) [13, 14] and MitoCarta3.0 [15, 16] databases for mitochondrial protein localization and pathway ontologies. 2D enrichment analysis of annotations was performed in Perseus to assess synaptosomal extraction quality and identify differentially enriched ontologies. We used the MitoCarta annotation to filter the mitochondrial proteins and generate subsets per localization. We conducted a Pearson correlation analysis of the LFQs of mitochondrial proteins in relation to tau protein. We then selected the results with a cutoff of 0.5 on the absolute Pearson coefficient to form groups of positively and negatively correlating (or uncorrelated) proteins. The overrepresentation of pathways at each mitochondrial localization was estimated as the fold-change between the pathway distribution observed from the total Mitocarta database and the distribution observed in the mitochondrial protein subset.
Statistical analysis:
Values are presented as the mean ± SEM; Statistical analyses were performed on raw data with Graphpad Prism software, Shapiro-Wilk tests were performed to test distribution normality. The level of significance was set to P < 0.05. Mitochondrial biosensor data were log-transformed, and multiple t-tests for control versus ePHF conditions were performed at each time point. Mass spectrometry data analysis: 2D annotation enrichment analysis was performed using Benjamini-Hochberg FDR Truncation with a 2% cutoff[18]. Pearson's correlation analysis was used to evaluate the correlation of proteins MAPT amounts. A cutoff with a correlation coefficient ≥ 0.5 was used to select correlating proteins for further analysis. Synapse active zone analysis: Comparison of counts, surfaces, and volumes was performed with t-tests or Mann-Whitney, respectively, for normal and non-normal distribution of data. Immunohistochemical analysis: one-way ANOVA of optical densities and mitochondrial data.