Drosophila stocks
Flies were grown at 25°C with a standard yeast-corn meal-dextrose diet. Aging experiments were conducted at 25°C, unless otherwise stated. Adult male flies were gathered in groups of 20–30 per vial for aging. Throughout the aging process, the food was refreshed every two days for the initial two weeks and subsequently replaced daily from the third week onward. The Drosophila stocks used are listed in Supplementary Table 1.
Drosophila brain immunostaining
Larvae or adult fly brains were dissected in PBS, fixed in 3.7% paraformaldehyde in PBS with 0.1% Triton X-100 on ice for 0.5 hour, and subsequently fixed at room temperature for an additional 0.5 hour. Following fixation, brains were rinsed in PBS with 0.4% Triton X-100 (PBST) and subjected to primary antibodies staining for 1 day at 4°C, then washed in PBST and incubated in secondary antibodies for 1 day at 4°C, followed by washing with PBST. In the TUNEL assay, after removal of the buffer, the TUNEL reaction mixture was added, incubated in a 37°C water bath for 1h, and briefly washed. Subsequently, brains were stained in PBST with 4',6-diamidino-2-phenylindole (DAPI) for 3 hours, briefly washed, and mounted with Prolong Gold (Thermo Fisher Scientific) on bridged slides, positioned as a line with the anterior side facing upward and both sides padded with double layers of Scotch transparent tape (except for a single layer for TH staining in the PAM cluster). For cleaved caspase 3 staining, third instar larvae of w1118 or hs-hid were heat-shocked in a 37°C water bath for 2 hours and allowed to recover for 5 hours before dissection. Imaging was performed using an FV3000 confocal microscope with consistent image settings for samples within each experiment. The primary antibodies used include rabbit anti-Tyrosine Hydroxylase TH (Pel Freeze, P40101-0, 1:500), rabbit anti-Cleaved Caspase-3 (Asp175) (Cell Signaling Technology, 9661, 1:500), rabbit anti-Cleaved Caspase-3 (Asp175) (5A1E) (Cell Signaling Technology, 9664, 1:500), mouse anti-Repo (DSHB, 8D12, 1:500), mouse anti-alpha-Tubulin (DSHB, 12G10, 1:5000), mouse anti-Malondialdehyde (Abcam, 11E3, ab243066, 1:500), mouse anti-4 Hydroxynonenal (Abcam, HNEJ-2, ab48506, 1:500), rabbit anti-α-syn (phospho S129) (Abcam, ab51253, 1:500).
Labkit-assisted Drosophila PAM cluster TH + neuron quantification
The TH + neurons within a single PAM cluster were imaged using FV3000 with 512x512 resolution and 0.34 µm slice interval for both TH and DAPI channels, generating z-stacks. Labkit training and TH + region prediction were performed on a computer featuring an NVIDIA Quadro P6000. Twenty representative z-stacks, encompassing a spectrum of TH signals and backgrounds, were vertically merged into a unified stack using Fiji/ImageJ. In Labkit (Fiji), the stack underwent more than 100 cycles of "scribbling-predicting-correcting" to train the TH + pixel classifier against backgrounds. The resulting classifier file with a size of 379 megabytes was applied consistently for subsequent TH + neuron analysis. For TH + region identification, the classifier file was loaded into Labkit to batch process a folder of z-stack TH images. The defects including noise and vacuoles on the Labkit-predicted mask images were further minimized using customized Matlab (Mathwork) code “Correct_Labkit_TH.m” (version 1.0, see the source code, instructions for installation and use, description of code dependencies and the test data in https://github.com/rmd13/FlyBrain_PAM_TH_DAPI_Labkit/ ). The code sequentially processes each slice of a Labkit-generated 0/1 mask image. It first smooths the mask using a Gaussian smoothing filter with a sigma of 1.5 to enhance the image quality. Following smoothing, a threshold of 0.25 is applied to the resulting image, thus only the pixels above this threshold are labeled as a new mask. This new mask slice is then dilated using a square-shaped structuring element with a width of 5 pixels. This step is crucial for filling in any small gaps or holes present within the TH + regions, ensuring that the mask is continuous. Additionally, the code identifies and addresses any larger holes that may still exist within the mask, provided these holes have an area of less than 200 pixels. These holes are filled to maintain the integrity of the mask. Finally, the mask is eroded using the same square-shaped structuring element with a width of 5 pixels. The above process helps to reduce the errors, resulting in a high-quality, refined mask suitable for subsequent image analysis steps. The processed mask images were imported into Imaris 8.4 (Bitplane) as a new channel alongside the raw images. TH + surfaces and DAPI spots were created using Imaris in the Labkit channel and DAPI channel, respectively. The number of TH + neurons in the PAM cluster was counted as DAPI spots located within the TH + surface by running the surface distance transformation extension (Imaris) outside the TH + surfaces.
Drosophila brain BODIPY C11 lipid peroxidation assay
Fly brains expressing pan-neuronal infrared fluorescent protein (mIFP) were dissected in PBS and transferred into in Eppendorf tube 1 containing 100 ul PBS. In Eppendorf tube 2, 0.5 ul of 5 mmol BODIPY C11 DMSO solution (Thermo Fisher Scientific, D3861) and 0.5 ul of 1% saponin (Sigma, S7900) were added into 350 ul PBS (B), mixed and transferred to the tube 1, which was then rolled at room temperature for 30 min. Following the rolling process, brains were briefly washed in PBS and mounted with PBS on a bridged slide using two layers of Scotch transparent tape, creating a 5 mm gap. Thick nail polish was used to secure the four corners of the coverslip, and additional PBS was added to fill any gaps if necessary. BODIPY C11 was immediately imaged in FV3000 using a 100x objective lens. The brain optic lobe was located and live-imaged using a 640 nm laser to determine the position of labeled neuronal membranes. Subsequently, images were acquired in the green channel (488 nm laser, 0.04% laser power, 515–545 nm emission) and red channel (561 nm laser, 0.02% laser power, 575–605 nm emission), respectively. Five images were acquired for each brain. For each group the brains were imaged within 1 hour. The lipid peroxidation index was analyzed as the ratio of the mean intensity of membrane area in the green channel to the mean intensity in the red channel using ImageJ/Fiji. For each brain, the lipid peroxidation index from five images was averaged. A pseudo-colored image was generated by creating a ratio channel and masking out the unstained area in Imaris.
Drosophila daily locomotor activity assay
Fly food, extracted from a vial, was trimmed into two semi-circles with a height of 5 mm, and then positioned on 3 layers of 5 cm x 5 cm tissue paper with smooth side up for a 0.5 hour drying period. To administer FSG67 (HY-112489, MedChemExpress LLC), 10 µl of 0 mmol,1 mmol, 2.5 mmol, or 5 mmol FSG67 solution in PBS was introduced to the smooth side of fly food and evenly distributed until complete absorption. One end of clean glass tube for locomotor activity assay was inserted down vertically into the food and capped. Anesthetized enclosed flies were individually transferred into each tube, and then the tube was blocked with a sponge on the opposite side. These loaded glass tubes were then affixed to the DAM2 Drosophila activity monitors (TriKinetics). The locomotor activities were recorded at a frequency of 10 s over a period of one to three weeks, maintaining a 12-hour light/dark cycles of LED illumination controlled via an Arduino-controlled relay by the same computer. The food was replaced every three days. Actograms captured during this period were analyzed using the ActogramJ plugin 80 in ImageJ/Fiji. Daily locomotor activities were further analyzed and plotted using Excel 2010 and GraphPad Prism 6.01.
Western blot
Fly brains were dissected in PBS and homogenized with pestles in brain lysis buffer (Tris-HCl, pH 8.0 10 mmol, NaCl 200 mmol, Triton X-100 1%, EDTA 5 mmol, Glycerol 5%, PMSF 0.5 mmol, DTT 1 mmol, protease inhibitor cocktail (Roche, 11873580001)). Subsequently, an equal volume of 2X laemmli loading buffer (Tris-HCl, pH 6.8, 125 mmol, bromophenol blue 0.02%, SDS 4%, glycerol 20%, β-mercaptoethanol 10%) was added and heated at 50oC for 0.5 hour. For detection of α-syn oligomers, fly brains were dissected in PBS and cross-linked in same-day prepared buffer A (HEPES 20 mmol pH 8.5, KCl 120 mmol, EDTA 2 mmol, sucrose 0.25 M, glycerol 1%, Dimethyl dithiobispropionimidate (DTBP) 4 mmol, protease inhibitor cocktail (Roche)) on ice for 1h. Then reaction was halted by adding 10 mmol Tris-HCl pH 8.8 for 10 min on ice. Brains were homogenized with a pestle, and an equal volume of 2X Laemmli loading buffer was added without β-mercaptoethanol or DTT, followed by heating at 50oC for 0.5 hour. The samples were loaded into Mini Protean TGX (stain-free) 4–20% gel (Bio-Rad, 4568095) to run for 100V 1.5 hour. The gel was UV-activated and transferred onto PVDF membrane using transfer buffer (Tris 25 mmol, Glycine 192 mmol, 20% methanol) at 100V for 1.5 hour. The membrane was fixed in PBS with 3.7% PFA and 0.025% glutaraldehyde for 0.5 hour, stain-free imaged, and blocked in 5% milk in Tris-buffered saline with 0.1% Tween-20 (TBST). Primary antibodies used include mouse anti-α-syn (BD 610787, 1:1000), rabbit anti-Gpi (Merck, HPA024305, 1:1000), rabbit anti-LDH (Thermo Fisher,PA5-26531, 1:1000), and secondary antibodies include anti-mouse HRP (CST, 7076S, 1:3000) and anti-rabbit HRP (Amersham, NA934-1ML, 1:3000). The HRP was detected using WesternBright Sirius in ChemiDoc (Bio-rad). The membrane was subsequently re-blotted with mouse anti-alpha tubulin (DSHB, 12G10, 1:5000). Image was analyzed using Image Lab (Bio-Rad) and ImageJ/Fiji, and the results were plotted in GraphPad prism.
Mito-roGFP2-Orp1 imaging for H2O2
Retina expressing mito-roGFP2-Orp1 were dissected in PBS and fixed in PBS with 3.7% PFA, 0.1% Triton X-100 and 20 mmol N-Ethylmaleimide (Thermo Fisher Scientific, 23030) for 0.5 hour on ice, followed by another 0.5 hour at room temperature. The fixed retina was washed in PBST with 5% goat serum overnight at 4oC and then was mounted with Prolong Gold anti-fade mountant (Thermo Fisher Scientific, P10144). Mito-roGFP2-Orp1 was imaged by exciting with a 405 nm or 488 nm laser, respectively, and collecting 500–530 nm emission light. The H2O2 index was determined by the ratio of mean intensity of the mitochondria in the two channels using ImageJ/Fiji.
MitoTimer imaging for cumulative redox history
Brains were dissected in PBS and fixed in PBS with 3.7% PFA and 0.1% Triton X-100 for 0.5 hour on ice and an additional 0.5 hour at room temperature. Following fixation, the brains were washed in PBST with 5% goat serum and DAPI overnight at 4oC and then mounted with Prolong Gold anti-fade mountant (Thermo Fisher Scientific, P10144). The green channel (488 nm laser, 500–540 nm emission) and the red channel (561 nm laser, 570–620 nm emission) were imaged on the cortex layer of the optic lobe. The ratio of the mean intensity of MitoTimer between the red and the green channel was analyzed using ImageJ/Fiji.
Drosophila climbing assay and quantification
The climbing assay was conducted on a customized workstation composed of a background white foam, side LED light, bottom light, 50 ml glass cylinders, an elastic cushion, and a Nikon digital camera securely affixed to a tripod. A sponge pad was positioned in the inner bottom of the cylinder to minimize potential harm to the flies during the climbing assay. 10 ~ 20 flies were flipped into a capped cylinder, tapped to the bottom and allowed to climb for 5 s, following which an image was promptly captured using the camera. The average climbing height for all the images was analyzed using a customized FlySpotter program (Srinivas Gorur-Shandilya, https://github.com/sg-s/fly-spotter) and graphically represented using GraphPad prism.
Real-time PCR for quantitative of fly brain transcripts
Fly brains of 3-weeks old were dissected in PBS, with trachea sacs and fat bodies detached, were subsequently transferred into RNAlater (Thermo Fisher Scientific, R0901). Following removal of excess fluid, RNA from the brain was extracted using TRIzol™ Reagent (Thermo Fisher Scientific, 15596026). The extracted RNA was treated with dsDNase (Thermo Fisher Scientific, EN0771). Subsequently, cDNA was prepared using Invitrogen SuperScripII First-Strand Synthesis System for RT-PCR (11904-018). qPCR was performed using iQ™ SYBR Green Supermix (Bio-rad, 1708882) and LightCycler 96 Instrument (Roche). The data was analyzed using LightCycler 96 software (Roche). RPL32 served as an internal control for mRNA quantification. The qPCR primers used include mino-F1: CAAGCCATCTGCCAGGGTCC, mino-R1: GACATCACAGAGGTGGCTGCTG, RpL32-qF1: ATGCTAAGCTGTCGCACAAATG, RpL32-qR1: GCTTGTTCGATCCGTAACCG.
Synuclein Preformed fibrils preparation
15µl of 2mg/ml synuclein PFF (StressMarq SPR-324) aliquoted into screw-capped tubes were sonicated in an ultrasonic bath sonicator for 2.5h at the following conditions: Sweep, 37Hz frequency, 60% power. Water was changed at 30mins interval to maintain the water temperature at 15°C.
Mouse primary neuron culture and staining
Mice-related studies were approved by and conformed to the guidelines of the Institutional Animal Care Committee (IACUC) of the Nanyang Technological University Lee Kong Chian School of Medicine. Embryonic day 17.5 mouse fetuses from C57BL/6 were obtained. The cortices were isolated and dissociated with papain (LS003119, Worthington) for 30 min at 37°C. Papain was removed and cortices were washed with DMEM/FBS and spin down at 1,000rpm, 5 mins. Cells were titrated, spin down and resuspended in Neurobasal medium supplemented with B27 and GlutaMAX (Gibco). 80,000 cells/ well were plated. At day 7, mice primary cortical neurons were treated with 1µg/ml α-syn monomers (SPR-323, StressMarq) or 1µg/ml synuclein PFF (SPR-322, StressMarq) with or without 75 mmol FSG (HY-112489, MedChemExpress LLC) for 2 weeks. Following treatment, cells were fixed in 4% PFA/4% sucrose/PBS for 30 minutes at room temperature, then washed three times with PBS. Subsequently, cells were blocked in 0.2 M glycine, 0.1 mg/ml saponin, and 30 mg/ml BSA in PBS for 45 minutes. Primary antibodies staining was carried out in antibody diluent (0.1 mg/ml saponin and 1 mg/ml BSA in PBS) for 1 hour at room temperature using anti-Malondialdehyde antibody (Abcam, 11E3, ab243066, 1:500), anti-4-Hydroxynonenal antibody (Abcam, HNEJ-2, ab48506, 1:500) and anti-α-syn phospho S129 (Abcam, ab51253, 1:500). After washing three times with PBS, cells were incubated with secondary antibodies in antibody diluent for 1 hour, followed by four washes with PBS. Finally, cells were stained with BODIPY 493/503 (Thermo Fisher Scientific, D-3922, 1:1000) and 1 µg/ml DAPI, mounted, and imaged using an FV3000 confocal microscope (Olympus). For lipid peroxidation assay, 5 mmol BODIPY C11 was added to the culture medium of glass-bottom culture dish in 1:1000 dilutions and incubated for 0.5 hour, then directly imaged in the green and red channel respectively. The ratio of mean intensity in the cell was analyzed using ImageJ/Fiji.
Statistics
Statistical analyses were conducted using Prism 8 (GraphPad) and Matlab (MathWorks). For the genetic screening, the Anderson-Darling test was applied to assess the non-normal distribution of all the data, followed by the Mann-Whitney U-test. The p-values were adjusted by the Benjamini-Hochberg method using the Matlab function padj = PVAL ADJUST (p-values, ‘BH’), where p is the input vector of all the p-values (fakenmc/pval_adjust, version 1.2.0.2, by Nuno Fachada. https://github.com/nunofachada/pval_adjust). One-way or two-way ANOVA, supplemented by Tukey’s and Dunnett’s post hoc test, was used for multi-group comparisons. All tests were two-tailed. Sample sizes are specified in the figure legends. Data are presented as mean ± S.D. Significance levels are *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.