{"id":195486,"date":"2025-10-01T20:02:21","date_gmt":"2025-10-01T20:02:21","guid":{"rendered":"https:\/\/www.newsbeep.com\/us\/195486\/"},"modified":"2025-10-01T20:02:21","modified_gmt":"2025-10-01T20:02:21","slug":"large-scale-visualization-of-%ce%b1-synuclein-oligomers-in-parkinsons-disease-brain-tissue","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/us\/195486\/","title":{"rendered":"Large-scale visualization of \u03b1-synuclein oligomers in Parkinson\u2019s disease brain tissue"},"content":{"rendered":"<p>Autofluorescence suppression and high-sensitivity microscopy reveals nanoscale assemblies in human brain tissue<\/p>\n<p>An overview of the ASA\u2013PD pipeline is shown in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig1\" rel=\"nofollow noopener\" target=\"_blank\">1<\/a>. In brief, the aim is to capture spatial data over the entire scale of structure sizes most critical in PD, from individual cells to small aggregates (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig1\" rel=\"nofollow noopener\" target=\"_blank\">1a<\/a>). Detailed descriptions of the sample preparation steps are described in the <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"section anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Sec9\" rel=\"nofollow noopener\" target=\"_blank\">Methods<\/a>. First, 8-\u03bcm-thick brain tissue sections were mounted on glass slides, stained and then processed in the five stages illustrated in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig1\" rel=\"nofollow noopener\" target=\"_blank\">1b<\/a>: (1) background suppression, (2) enhanced imaging, (3) feature detection, (4) analytical computation and (5) spatial distribution analysis, where the first two steps contain the experimental portion of our workflow and steps 3\u20135 perform image-processing tasks and analysis.<\/p>\n<p>Fig. 1: ASA\u2013PD.<a class=\"c-article-section__figure-link\" data-test=\"img-link\" data-track=\"click\" data-track-label=\"image\" data-track-action=\"view figure\" href=\"https:\/\/www.nature.com\/articles\/s41551-025-01496-4\/figures\/1\" rel=\"nofollow noopener\" target=\"_blank\"><img decoding=\"async\" aria-describedby=\"Fig1\" src=\"https:\/\/www.newsbeep.com\/us\/wp-content\/uploads\/2025\/10\/41551_2025_1496_Fig1_HTML.png\" alt=\"figure 1\" loading=\"lazy\" width=\"685\" height=\"788\"\/><\/a><\/p>\n<p>a, ASA-PD is an imaging and analysis method for detecting protein aggregates in tissue down to nanoscale aggregates. b, The five main steps for imaging and analysis. Background suppression and enhanced imaging improve the signal-to-noise ratio such that aggregates can be detected and quantified in the analysis pipeline, including the spatial distributions relative to cell-specific markers. BG, background. Panels a and b created with <a href=\"http:\/\/www.biorender.com\" rel=\"nofollow noopener\" target=\"_blank\">BioRender.com<\/a>.<\/p>\n<p>Observing protein aggregates is relatively routine in in vitro conditions<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" title=\"Lee, J.-E. et al. Mapping surface hydrophobicity of &#x3B1;-synuclein oligomers at the nanoscale. Nano Lett. 18, 7494&#x2013;7501 (2018).\" href=\"#ref-CR38\" id=\"ref-link-section-d92682793e1345\">38<\/a>,<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" title=\"Whiten, D. R. et al. Nanoscopic characterisation of individual endogenous protein aggregates in human neuronal cells. ChemBioChem 19, 2033&#x2013;2038 (2018).\" href=\"#ref-CR39\" id=\"ref-link-section-d92682793e1345_1\">39<\/a>,<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 40\" title=\"Sahl, S. J. et al. Delayed emergence of subdiffraction-sized mutant huntingtin fibrils following inclusion body formation. Q. Rev. Biophys. 49, e2 (2016).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR40\" id=\"ref-link-section-d92682793e1348\" rel=\"nofollow noopener\" target=\"_blank\">40<\/a>, but detecting small species in vivo poses a challenge owing to the poor signal-to-noise ratio in tissue. High background intensity, caused by tissue autofluorescence, acts as a noise floor that obscures the presence of dim objects such as oligomeric species. This noise effectively implements a brightness filter that leaves only large protein aggregates, with many attached fluorescent antibodies, as detectable species. To reduce the high autofluorescence of human brain tissue that inhibits sensitive imaging, we deployed Sudan Black B (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig2\" rel=\"nofollow noopener\" target=\"_blank\">2a<\/a>), a fat-soluble diazo dye and well-known autofluorescence quencher on untreated brain tissue sections<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 41\" title=\"Oliveira, V. C. et al. Sudan Black B treatment reduces autofluorescence and improves resolution of in situ hybridization specific fluorescent signals of brain sections. Histol. Histopathol. 25, 1017&#x2013;1024 (2010).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR41\" id=\"ref-link-section-d92682793e1355\" rel=\"nofollow noopener\" target=\"_blank\">41<\/a>. Under optimized conditions, 10\u2009min of incubation with 0.1% Sudan Black led to a 93% reduction in background autofluorescence for 561\u2009nm laser excitation (26\u2009W\u2009cm\u22122 illumination intensity), corresponding to a decrease in median detected photon counts from 4,400\u2009\u00b1\u20091,040 photons \u00b1 median absolute deviation (MAD) to 333\u2009\u00b1\u200947 photons (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig2\" rel=\"nofollow noopener\" target=\"_blank\">2b<\/a>) (the background reduction for other excitation colours (488, 561\u2009nm), treatment times and concentrations are shown in Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">1<\/a>). Next, we repeated this background suppression step on antibody-labelled samples and evaluated various antibodies against multiple forms of \u03b1-synuclein for specificity and detectability (Supplementary Figs. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2<\/a> and <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">3<\/a> and Supplementary Table <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">1<\/a>). The background reduction by Sudan Black facilitated the reliable detection of small features in images with a vastly improved signal-to-noise ratio for some of the antibodies tested, as shown in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig2\" rel=\"nofollow noopener\" target=\"_blank\">2c<\/a>.<\/p>\n<p>Fig. 2: Background suppression and high-sensitivity microscopy in human brain tissue.<a class=\"c-article-section__figure-link\" data-test=\"img-link\" data-track=\"click\" data-track-label=\"image\" data-track-action=\"view figure\" href=\"https:\/\/www.nature.com\/articles\/s41551-025-01496-4\/figures\/2\" rel=\"nofollow noopener\" target=\"_blank\"><img decoding=\"async\" aria-describedby=\"Fig2\" src=\"https:\/\/www.newsbeep.com\/us\/wp-content\/uploads\/2025\/10\/41551_2025_1496_Fig2_HTML.png\" alt=\"figure 2\" loading=\"lazy\" width=\"685\" height=\"621\"\/><\/a><\/p>\n<p>a, Background suppression is achieved with the autofluorescence quencher Sudan Black (SB). b, Box plots showing the IQR and 5th\u201395th percentile bounds of autofluorescence (AF) intensity before (median of 4,400) and after treatment with 0.1% SB (median of 333). N\u2009=\u2009180 images per sample. c, Before quenching, the fluorescence from Alexa Fluor 568 labelled small aggregates is masked by the background autofluorescence. After quenching, small aggregates can be easily visualized (both images excited at 561\u2009nm, 26\u2009W\u2009cm\u22122). d, A high NA objective collects a larger amount of light from the sample. e, The modelled signal-to-noise ratio for imaging punctate objects in post-quenched tissue background at 100\u00d7 magnification across a range of NAs of objectives. Only at high NA (&gt;1) large aggregates and oligomers become detectable. f, Images of p-syn stained PD tissue with 40\u00d7 magnification, NA\u2009=\u20090.75 (top) and 100\u00d7, NA\u2009=\u20091.49 (bottom). Close-ups show that the same small aggregate is clearly visible at high magnification and high NA. g, Images of p-syn stained PD tissue with no background suppression and low NA (left), background suppression implemented and low NA (middle) and background suppression implemented and high NA (right). Several example puncta are shown in the closeups (oligomers) after background suppression is implemented and a high NA objective is used.<\/p>\n<p>To visualize the \u03b1-synuclein aggregates most associated with PD, we used an antibody targeting phosphorylated \u03b1-synuclein at serine 129 (hereafter called p-syn). This post-translational modification promotes inclusion formation and\/or toxicity in human cells<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 42\" title=\"Luk, K. C. et al. Exogenous &#x3B1;-synuclein fibrils seed the formation of Lewy body-like intracellular inclusions in cultured cells. Proc. Natl Acad. Sci. USA 106, 20051&#x2013;20056 (2009).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR42\" id=\"ref-link-section-d92682793e1435\" rel=\"nofollow noopener\" target=\"_blank\">42<\/a>, Drosophila<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 43\" title=\"Chen, L. &amp; Feany, M. B. &#x3B1;-Synuclein phosphorylation controls neurotoxicity and inclusion formation in a Drosophila model of Parkinson disease. Nat. Neurosci. 8, 657&#x2013;663 (2005).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR43\" id=\"ref-link-section-d92682793e1441\" rel=\"nofollow noopener\" target=\"_blank\">43<\/a> and rodent models<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 44\" title=\"Kahle, P. J. et al. Hyperphosphorylation and insolubility of &#x3B1;&#x2010;synuclein in transgenic mouse oligodendrocytes. EMBO Rep. 3, 583&#x2013;588 (2002).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR44\" id=\"ref-link-section-d92682793e1445\" rel=\"nofollow noopener\" target=\"_blank\">44<\/a>,<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 45\" title=\"Gorbatyuk, O. S. et al. The phosphorylation state of Ser-129 in human &#x3B1;-synuclein determines neurodegeneration in a rat model of Parkinson disease. Proc. Natl Acad. Sci. USA 105, 763&#x2013;768 (2008).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR45\" id=\"ref-link-section-d92682793e1448\" rel=\"nofollow noopener\" target=\"_blank\">45<\/a>. Further, p-syn forms the vast majority of all insoluble \u03b1-synuclein aggregates in the PD brain<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 46\" title=\"Fujiwara, H. et al. &#x3B1;-Synuclein is phosphorylated in synucleinopathy lesions. Nat. Cell Biol. 4, 160&#x2013;164 (2002).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR46\" id=\"ref-link-section-d92682793e1452\" rel=\"nofollow noopener\" target=\"_blank\">46<\/a>. Given this link between p-syn and pathology in synucleinopathies, we tested a variety of antibodies (Supplementary Table <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">1<\/a>), including two complementary antibodies targeting the pS129 epitope of \u03b1-synuclein raised in two species (rabbit, AB_2270761, and mouse, AB_2819037). The AB_2819037 antibody showed characteristic Lewy pathology in both DAB and immunofluorescence staining and were shown to be specific through substantial co-localization with a second antibody for total \u03b1-synuclein (AB_2832854) (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2<\/a>). The final p-syn antibody selection, AB_2819037, was selected because of (1) the degree of coincidence of the p-syn antibody compared with total \u03b1-synuclein; (2) co-localization with other disease-related proteins, such as ubiquitin and p62; and (3) the demonstration of antibody specificity for human \u03b1-synuclein based on mouse tissue with the overexpression or knockout of human \u03b1-synuclein<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 47\" title=\"Janezic, S. et al. Deficits in dopaminergic transmission precede neuron loss and dysfunction in a new Parkinson model. Proc. Natl Acad. Sci. USA 110, E4016&#x2013;E4025 (2013).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR47\" id=\"ref-link-section-d92682793e1463\" rel=\"nofollow noopener\" target=\"_blank\">47<\/a>. Furthermore, we confirmed (via electron microscopy and fluorescence imaging) that purified p-syn can aggregate in vitro, and form \u03b2-sheet rich 10-nm assemblies<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 48\" title=\"Needham, L.-M. et al. ThX&#x2014;a next-generation probe for the early detection of amyloid aggregates. Chem. Sci. 11, 4578&#x2013;4583 (2020).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR48\" id=\"ref-link-section-d92682793e1467\" rel=\"nofollow noopener\" target=\"_blank\">48<\/a>. These recombinant p-syn protein aggregates can be detected by the same AB_2819037 antibody (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">4<\/a>).<\/p>\n<p>One way to improve the signal-to-noise ratio beyond reducing the overall background intensity is by improving the light-collection efficiency of the imaging system. In most microscopes, the least efficient step in light collection occurs at the objective lens of the microscope and is encoded in the numerical aperture (NA). Using a high NA objective lens has two main impacts: first, the NA scales with the collection angle of collected light<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 49\" title=\"Born, M. &amp; Wolf, E. Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light. (Cambridge Univ. Press, 1999).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR49\" id=\"ref-link-section-d92682793e1477\" rel=\"nofollow noopener\" target=\"_blank\">49<\/a> (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig2\" rel=\"nofollow noopener\" target=\"_blank\">2d<\/a> and Supplementary equation (<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">3<\/a>)), and thus, more photons from the sample are collected at high NA. Second, increasing the NA improves the image resolution<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 50\" title=\"Abbe Ernst. beitr&#xE4;ge zur theorie des mikroskops und der mikroskopischen wahrnehmung. Arch. mikrosk. Anat. 9, 413&#x2013;468 (1873).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR50\" id=\"ref-link-section-d92682793e1487\" rel=\"nofollow noopener\" target=\"_blank\">50<\/a> (Supplementary equation (<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">8<\/a>)). For imaging in tissue, we deployed a 1.49 NA oil-immersion, 100\u00d7 microscope objective lens often used in single-molecule fluorescence applications<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 51\" title=\"Single-Molecule Techniques: a Laboratory Manual (Cold Spring Harbor Laboratory Press, 2008).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR51\" id=\"ref-link-section-d92682793e1495\" rel=\"nofollow noopener\" target=\"_blank\">51<\/a>. The result is an overall increase in the signal-to-noise ratio for all objects, which is particularly important for the nanoscale assemblies that fall below the detectability range for lower NA objectives (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig2\" rel=\"nofollow noopener\" target=\"_blank\">2e<\/a>), such as the air objectives most often used in slide scanners for clinical applications<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 52\" title=\"Hanna, M. G. et al. Whole slide imaging equivalency and efficiency study: experience at a large academic center. Mod. Pathol. 32, 916&#x2013;928 (2019).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR52\" id=\"ref-link-section-d92682793e1502\" rel=\"nofollow noopener\" target=\"_blank\">52<\/a>. Figure <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig2\" rel=\"nofollow noopener\" target=\"_blank\">2f<\/a> compares a 0.75 NA 40\u00d7 air objective lens (top) with the 1.49 NA 100\u00d7 oil objective lens used in this study (bottom) for the same tissue sample stained for phosphorylated \u03b1-synuclein and quenched with 0.1% Sudan Black. The effect of background suppression and increased light collection using a high NA are shown in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig2\" rel=\"nofollow noopener\" target=\"_blank\">2g<\/a>. In these images, a wide variety of object sizes become visible; which we divide into two classes on the basis of their apparent size relative to the diffraction limit. Specifically, we define \u2018large\u2019 as greater than the optical diffraction limit of visible light, spanning ~200\u2009nm to tens of microns, and \u2018nanoscale\u2019 as objects below the optical diffraction limit (&lt;200\u2009nm). The fluorescence signal from the latter manifests as small symmetric puncta in the image. Three examples of the nanoscale objects that become visible via ASA\u2013PD are highlighted in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig2\" rel=\"nofollow noopener\" target=\"_blank\">2g(i\u2013iii)<\/a>. We refer to the latter objects as protein assemblies.<\/p>\n<p>Applying the ASA\u2013PD protocol within tissue revealed hundreds of detectable fluorescent puncta per field of view (FOV) (55\u2009\u00d7\u200955\u2009\u00b5m2) in both PD and HC samples (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">5<\/a>). To perform statistically robust comparisons between samples, we developed a computationally efficient method for detecting and quantifying fluorescent species. This open-source analysis pipeline<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 53\" title=\"Fu, B. et al. RASP: optimal single puncta detection in complex cellular backgrounds. J. Phys. Chem. B 128, 3585&#x2013;3597 (2024).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR53\" id=\"ref-link-section-d92682793e1524\" rel=\"nofollow noopener\" target=\"_blank\">53<\/a> facilitates the rapid processing of large image libraries, facilitating transparent, shareable and verifiable results.<\/p>\n<p>A schematic illustrating the analysis method and its validation is shown in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3<\/a>. In brief, the analysis pipeline identifies features in an image, classifies them as either large aggregates or protein assemblies and quantifies details such as brightness, size and position<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 53\" title=\"Fu, B. et al. RASP: optimal single puncta detection in complex cellular backgrounds. J. Phys. Chem. B 128, 3585&#x2013;3597 (2024).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR53\" id=\"ref-link-section-d92682793e1534\" rel=\"nofollow noopener\" target=\"_blank\">53<\/a>. A detailed description of the analysis is provided in Supplementary Information Note <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">3.1<\/a> and Supplementary Figs. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">6<\/a>\u2013<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">12<\/a>. Figure <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3a<\/a> shows a typical PD image containing nano and microscale features. Microscale aggregates, such as Lewy bodies and Lewy neurites, are extremely bright in the dataset. These objects can be segmented with a simple intensity threshold after a background subtraction step (large-object pipeline in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3b<\/a> and Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">7<\/a>). As large objects sometimes extend over multiple z-slices, the mask in each plane is multiplied by a segmented maximum-intensity projection from the z-stack. Smaller aggregates appear as dim, diffraction-limited puncta, and it is crucial to account for local background heterogeneity for detection (small-aggregate pipeline in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3b<\/a>). To do so, we applied a bandpass filter to each image which selects features on the scale of the diffraction limit<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 54\" title=\"Hosken, J. W. J. Ricker wavelets in their various guises. First Break 6, (1988).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR54\" id=\"ref-link-section-d92682793e1560\" rel=\"nofollow noopener\" target=\"_blank\">54<\/a> (Supplementary Figs. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">6<\/a> and <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">9<\/a>). Next, a threshold was used to create a mask containing only small objects. Objects with a footprint larger than the diffraction limit<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 49\" title=\"Born, M. &amp; Wolf, E. Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light. (Cambridge Univ. Press, 1999).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR49\" id=\"ref-link-section-d92682793e1571\" rel=\"nofollow noopener\" target=\"_blank\">49<\/a> were reclassified as \u2018large\u2019 for subsequent analysis. Finally, the large and small aggregate masks were compared, and overlapping objects were removed from the nanoscale object dataset. Figure <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3c<\/a> shows an overlay of the detected objects on the original image, and a gallery of diffraction-limited puncta is shown in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3d<\/a>.<\/p>\n<p>Fig. 3: Aggregate detection pipeline.<a class=\"c-article-section__figure-link\" data-test=\"img-link\" data-track=\"click\" data-track-label=\"image\" data-track-action=\"view figure\" href=\"https:\/\/www.nature.com\/articles\/s41551-025-01496-4\/figures\/3\" rel=\"nofollow noopener\" target=\"_blank\"><img decoding=\"async\" aria-describedby=\"Fig3\" src=\"https:\/\/www.newsbeep.com\/us\/wp-content\/uploads\/2025\/10\/41551_2025_1496_Fig3_HTML.png\" alt=\"figure 3\" loading=\"lazy\" width=\"685\" height=\"355\"\/><\/a><\/p>\n<p>a, A typical sample image containing features of various sizes and intensities, that is, Lewy neurites, micron-scale aggregates and sub-diffraction-limit oligomers. b, The aggregate detection pipeline for measuring large aggregates (top) and subdiffraction-sized features (bottom). The large object pipeline combines the z-projected intensity data with background-subtracted and threshold individual slices to generate a binary mask. Small aggregates are identified using a Ricker wavelet filter that acts as a bandpass, emphasizing small spots, which are then measured with a threshold and sorted by the number of pixels above the background. Features larger than the diffraction limit are reclassified as \u2018large\u2019 and features overlapping between the two masks are removed from the small aggregate pool. c, The large (green) and oligomer (blue) masks shown over the original image. d, The representative oligomers detected from c. e\u2013h, The quantification of the pipeline performance using simulated images of diffraction-limited spots on a noisy background at various signal-to-noise ratios. The grey shaded region represents the lower quartile determined from experimental conditions, while the green and pink shaded area represents the mean \u00b1 s.d. The intensity and average background values for all detected peaks in simulated images were estimated by quantifying the pixel values around the detected peaks (pink curve) and by fitting a symmetric two-dimensional-Gaussian function with nonlinear least squares fitting (green). The presented values were obtained by averaging the mean and s.d. within the IQR of the experimental CNR data (Q1\u2009=\u20094.2, Q3\u2009=\u20098.1).<\/p>\n<p>To evaluate the performance of the pipeline for detecting and characterizing nanoscale assemblies, we simulated images of puncta on noisy backgrounds at various signal-to-noise levels based on empirically determined parameters (Supplementary Note <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">3.2<\/a>, Simulations). In the signal-to-noise range of our data, approximately ~4\u20138, the algorithm\u2019s sensitivity was &gt;82%, with a precision of &gt;94% (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3e,f<\/a>). At the same time, the relative error for estimating the local background per puncta outperformed nonlinear least-squares Gaussian fitting in this low signal-to-noise regime where Gaussian fitting performed poorly on aberrantly detected pixels, that is, false positives (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig3\" rel=\"nofollow noopener\" target=\"_blank\">3g,h<\/a>).<\/p>\n<p>ASA\u2013PD reveals a disease-specific shift in the nanoscale population of \u03b1-synuclein assemblies<\/p>\n<p>To characterize the distributions of \u03b1-synuclein in brain tissue, we selected three PD brains (Braak stage 6) and three HC brains for imaging (Supplementary Table <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2<\/a>). Tissue sections from the anterior cingulate cortical gyrus were put through the ASA\u2013PD process. At this point, three principal regions within the grey matter were selected for investigation. At each of these regions, nine FOVs were captured in a 3\u2009\u00d7\u20093 grid with a lateral separation of 150\u2009\u03bcm to avoid any spatial overlap (each image covers 55\u2009\u00d7\u200955\u2009\u00b5m2). In total, 17 axial planes were recorded using a 500\u2009nm step size (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig4\" rel=\"nofollow noopener\" target=\"_blank\">4a<\/a> and <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"section anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Sec9\" rel=\"nofollow noopener\" target=\"_blank\">Methods<\/a>). This process generated 13,770 high-resolution images (&gt;41.6\u2009mm2) that were manually validated to ensure the sample was in focus and the tissue contained no notable tears or defects. After this verification step, 12,028 images remained, 87.5% of the original dataset (5,954 PD and 6,074 HC images). These images were analysed as described in the previous section to map large aggregates (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig4\" rel=\"nofollow noopener\" target=\"_blank\">4c,d<\/a>) and nanoscale assemblies (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig4\" rel=\"nofollow noopener\" target=\"_blank\">4e,f<\/a>). Negative control samples, lacking primary antibodies, were also tested using PD tissue to quantify the degree of false positives caused by residual autofluorescence and unbound secondary antibodies (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">12<\/a>).<\/p>\n<p>Fig. 4: Aggregate distributions in human brain tissue.<a class=\"c-article-section__figure-link\" data-test=\"img-link\" data-track=\"click\" data-track-label=\"image\" data-track-action=\"view figure\" href=\"https:\/\/www.nature.com\/articles\/s41551-025-01496-4\/figures\/4\" rel=\"nofollow noopener\" target=\"_blank\"><img decoding=\"async\" aria-describedby=\"Fig4\" src=\"https:\/\/www.newsbeep.com\/us\/wp-content\/uploads\/2025\/10\/41551_2025_1496_Fig4_HTML.png\" alt=\"figure 4\" loading=\"lazy\" width=\"685\" height=\"331\"\/><\/a><\/p>\n<p>a, The imaging of grey matter was performed in three areas, each area being a 3\u2009\u00d7\u20093 grid of z stacks (17 slices) spaced 150\u2009\u00b5m apart. b, The number of HCs and patients with PD (n\u2009=\u20093), number of tissue sections (n\u2009=\u200915) and number of images taken NHC\u2009=\u20096,074 and NPD\u2009=\u20095,954. c, Examples of analysed FOVs showing only the detected large aggregates. d, The number of large aggregates detected per patient over 1,800 FOVs (5.4\u2009mm2). The mean \u00b1 s.d. for large aggregates was 3,866\u2009\u00b1\u2009408 in HCs and 26,314\u2009\u00b1\u20097712 in PD, the means were compared by a two-tailed two-sample t-test, with P\u2009=\u20090.0147. e,f, Example FOVs of detected \u03b1-synuclein oligomers in HC and PD (Braak stage 6), respectively. g, The total number of \u03b1-synuclein aggregates in HC and PD tissues. The left panel shows oligomers (&lt;0.04\u2009\u03bcm2). The right panel shows large aggregates (&gt;0.04\u2009\u03bcm2). The typical Lewy neurites sizes (~5\u201330\u2009\u03bcm2) and Lewy bodies (~30\u2013300\u2009\u03bcm2) are shown for reference. h, Violin plot of brightness of detected oligomers truncated at 1.5\u00d7 IQR. Oligomers in HC had a median of 2,750 photons (MAD of 1,060) and of 3,700 photons (MAD of 1,690) for PD. The bright subpopulation of oligomers is shown in red for PD. i, The total number of detected oligomers per patient above this brightness threshold, 10,280 photons. Error bars are variation in boundary rejection percentage per patient, propagated. *P\u2009&lt;\u20090.05.<\/p>\n<p>From the ~12,000 images recorded across 30 tissue sections, we obtained a dataset containing more than 125,000 large aggregates and 1,260,000 nanoscale assemblies<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 35\" title=\"Andrews, R. et al. Direct visualisation of alpha-synuclein oligomers in human brain tissue&#x2014;raw data. Aligning Science Across Parkinsons &#010;                https:\/\/doi.org\/10.5281\/ZENODO.10610924&#010;                &#010;               (2024).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR35\" id=\"ref-link-section-d92682793e1750\" rel=\"nofollow noopener\" target=\"_blank\">35<\/a>,<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 36\" title=\"Andrews, R., Fu, B., Toomey, C. E., Breiter, J. C. &amp; Lee, S. F. Direct visualisation of alpha-synuclein oligomers in human brain tissue&#x2014;processed data. Aligning Science Across Parkinsons &#010;                https:\/\/doi.org\/10.5281\/ZENODO.10610657&#010;                &#010;               (2024).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR36\" id=\"ref-link-section-d92682793e1753\" rel=\"nofollow noopener\" target=\"_blank\">36<\/a>. From the ~400 FOVs (~1.2\u2009mm2), from each patient sample, the average number of large aggregates detected was ~tenfold higher in patients with PD than in the HC, with 26,314\u2009\u00b1\u20097712 in PD and 3,866\u2009\u00b1\u2009408 in HC, respectively (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig4\" rel=\"nofollow noopener\" target=\"_blank\">4d<\/a>). These aggregates were distributed over a broad range of sizes from 0.04 to 100\u2009\u00b5m2 in PD and 0.04 to 1\u2009\u00b5m2 in HC (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig4\" rel=\"nofollow noopener\" target=\"_blank\">4g<\/a>), where the aggregate sizes associated with Lewy pathology essentially exclusively found in PD samples, consistent with the original tissue classifications (Supplementary Table <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2<\/a>). The total number of detected nanoscale objects in PD and HCs were much more similar (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig4\" rel=\"nofollow noopener\" target=\"_blank\">4g<\/a>), with 682,826 and 582,026 objects, respectively (with densities 0.082\u2009objects per \u03bcm2 for PD and 0.067\u2009objects per \u03bcm2 for HC).<\/p>\n<p>While image resolution remains fundamentally diffraction-limited, the high sensitivity of ASA\u2013PD to dim puncta, coupled with their relative sparsity, allows the detection of ~10\u2009nm objects\u2014far below the diffraction limit. At this scale, the resolution obscures aggregate sizes; however, for larger aggregates, where the size and brightness can be measured, the two were strongly linearly proportional, R2\u2009&gt;\u20090.99 (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">13a<\/a>). We, therefore, characterized the distribution of nanoscale-object intensities as a proxy for the approximate size of these assemblies (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig4\" rel=\"nofollow noopener\" target=\"_blank\">4h<\/a>). The brightness distributions for all measured objects are shown in Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">13b<\/a> together with the estimated number of bound secondary antibodies, assuming each antibody contributes ~700 photons in our imaging conditions (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">14<\/a>). Relative to the HC, the median was larger for PD samples, 3,700 photons (MAD of 1,690) and 2,750 photons (MAD of 1,060), and the distribution of brightnesses in PD samples was also broader, characterized by its interquartile range (IQR) IQRPD\u2009=\u20094,280 photons compared with IQRHC\u2009=\u20092,690 for HCs. To determine if the distribution tail was reproducibly different between PD and HC samples, we defined a brightness threshold using the HC measurements (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig4\" rel=\"nofollow noopener\" target=\"_blank\">4h<\/a>). The number of nanoscale objects above this threshold (10,280 photons, equating to ~15 bound secondary antibodies) is shown in Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig4\" rel=\"nofollow noopener\" target=\"_blank\">4i<\/a>. This data represents ~10% of all measured PD assemblies but only 0.26% of those in HC (totalling 68,569 in PD and 1,518 in HC). The existence of this bright, disease-specific shift in the nanoscale population was highly robust by ASA\u2013PD and was observed consistently when testing different \u03b1-synuclein antibodies, two different brain banks (Queen Square Brain Bank for Neurological Disorders (QSBB) and Multiple Sclerosis and Parkinson\u2019s Brain Bank (Imperial), 12 individuals (6 PD and 6 HC), and using different antigen retrieval methods (formic acid and heat mediated epitope retrieval) (Supplementary Note <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">3.3<\/a>, Supplementary Figs. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">15<\/a>\u2013<a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">17<\/a> and Supplementary Tables <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">2<\/a> and <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">3<\/a>).<\/p>\n<p>Subpopulations of nanoscale \u03b1-synuclein assemblies are detectable by biochemical methods<\/p>\n<p>Our approach enables the direct visualization of nanoscale aggregates that are typically challenging to detect. To further investigate the nanoscale assemblies revealed by our approach and determine if the fraction of bright nanoscale aggregates found in disease PD tissue could be detected with orthogonal methods, we performed PLA, enzyme-linked immunosorbent assays (ELISA), size exclusion chromatography (SEC) and seed amplification assays (SAAs) in brain tissue samples.<\/p>\n<p>PLA can detect protein\u2013protein interactions using antibody-linked DNA probes<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 34\" title=\"Sekiya, H. et al. Wide distribution of alpha-synuclein oligomers in multiple system atrophy brain detected by proximity ligation. Acta Neuropathol. 137, 455&#x2013;466 (2019).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR34\" id=\"ref-link-section-d92682793e1837\" rel=\"nofollow noopener\" target=\"_blank\">34<\/a>. When these probes are adjacent, they produce an amplified signal that can be visualized using fluorescence microscopy (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">19a<\/a>). This approach can be used to detect nanoscale assemblies of \u03b1-synuclein by amplifying the signal from \u03b1-synuclein 211 antibodies that are in close proximity. PLA was performed on 13 brain sections from the anterior cingulate gyrus, comprising six late Braak stage 5\u20136 PD and seven HC samples (Supplementary Table <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">3<\/a>), and imaged (20\u00d7 magnification, NA 0.75). Four images of the cingulate cortex were taken per sample and fluorescent puncta were quantified based on their intensity and a minimum size threshold of 0.9\u2009\u00b5m. Representative images and the puncta density is shown in Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">19b,c<\/a> plotted per sample. The average number of puncta revealed an enriched population of aggregated \u03b1-synuclein in PD samples compared with HC samples, consistent with the ASA-PD data.<\/p>\n<p>Next, brain lysates were fractionated using SEC to separate soluble \u03b1-synuclein species by apparent molecular weight from the Braak stage five or six PD, and HC donors (three PD and three HC; Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">20a<\/a>). This was followed by ELISA on the fractions to quantify the absolute amount of \u03b1Syn per fraction. Fractions were then subjected to the SAA, which allows the amplification and detection of small amounts of aggregates present in a sample. Recombinant human monomeric \u03b1-synuclein was used for the amplification of templated aggregation from pre-existing aggregates, and the kinetics of the amplification reaction was monitored by Thioflavin T (ThT) binding and increase in its fluorescence intensity.<\/p>\n<p>The SEC-ELISA analysis revealed that total \u03b1-synuclein concentrations differed across high and low molecular weight fractions by two orders of magnitude but did not reveal statistical differences in the total \u03b1-synuclein in PD compared with controls, suggesting a similar amount of total protein (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">20b<\/a>). The SAA revealed that high molecular weight fractions (200\u2009kDa to 5\u2009MDa) from PD brains had significantly shorter lag times, indicating the presence of seed competent \u03b1Syn aggregates, compared with samples derived from healthy brain tissue. Physiological (low molecular weight) fractions, in contrast, showed no statistical differences in lag times between PD and HC samples (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">20d,e<\/a>). Comparisons between high molecular weight and low molecular weight fractions could not be made owing to altered \u03b1-synuclein concentrations. Therefore, there is a relatively small amount of aggregated \u03b1-synuclein (according to ELISA approx. 0.5% of total) both in physiological as well as disease tissue. In PD tissue, however, there is an apparent conversion of non-seed competent, or physiological, \u03b1-synuclein aggregates into seed competent aggregates.<\/p>\n<p>Finally, we validated the presence of Proteinase K-resistant fluorescent puncta to assess whether the observed aggregates exhibited distinct chemicophysical properties (Supplementary Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"supplementary material anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#MOESM1\" rel=\"nofollow noopener\" target=\"_blank\">21<\/a>). Notably, some bright puncta persisted after treatment, indicating a measurable degree of resistance to Proteinase K.<\/p>\n<p>Collectively, the ASA\u2013PD and amplification assay data confirm the presence of a population of small, soluble protein assemblies in the brain, which changes in PD samples, namely a subpopulation of bright assemblies has distinctive chemicophysical properties, such as their size and seed competence, and Proteinase K resistance.<\/p>\n<p>Disease-specific assemblies are spatially heterogeneous<\/p>\n<p>In addition to measuring object densities and size distributions, ASA\u2013PD can be used to analyse spatial distributions (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig5\" rel=\"nofollow noopener\" target=\"_blank\">5<\/a>). To determine if the heterogeneity reported for larger \u03b1-synuclein aggregates<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 4\" title=\"Braak, H. et al. Staging of brain pathology related to sporadic Parkinson&#x2019;s disease. Neurobiol. Aging 24, 197&#x2013;211 (2003).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR4\" id=\"ref-link-section-d92682793e1886\" rel=\"nofollow noopener\" target=\"_blank\">4<\/a>,<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 55\" title=\"Spillantini, M. G. et al. &#x3B1;-Synuclein in Lewy bodies. Nature 388, 839&#x2013;840 (1997).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR55\" id=\"ref-link-section-d92682793e1889\" rel=\"nofollow noopener\" target=\"_blank\">55<\/a> extends to nanoscale species in PD samples, we performed a spatial-clustering test, which compares the likelihood of encountering assemblies as a function of the distance from it<a data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 53\" title=\"Fu, B. et al. RASP: optimal single puncta detection in complex cellular backgrounds. J. Phys. Chem. B 128, 3585&#x2013;3597 (2024).\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#ref-CR53\" id=\"ref-link-section-d92682793e1893\" rel=\"nofollow noopener\" target=\"_blank\">53<\/a> (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig5\" rel=\"nofollow noopener\" target=\"_blank\">5a\u2013c<\/a>). Over 400 FoVs, 682,826 nanoscale objects were detected and characterized. On average, these species were found to cluster relative to a complete spatial random distribution. (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig5\" rel=\"nofollow noopener\" target=\"_blank\">5f<\/a>, blue); however, the disease-specific populations exhibited a substantially higher degree of clustering (68,569 aggregates; Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig5\" rel=\"nofollow noopener\" target=\"_blank\">5f<\/a>, red).<\/p>\n<p>Fig. 5: Spatial distribution of oligomers with respect to different brain cell types.<a class=\"c-article-section__figure-link\" data-test=\"img-link\" data-track=\"click\" data-track-label=\"image\" data-track-action=\"view figure\" href=\"https:\/\/www.nature.com\/articles\/s41551-025-01496-4\/figures\/5\" rel=\"nofollow noopener\" target=\"_blank\"><img decoding=\"async\" aria-describedby=\"Fig5\" src=\"https:\/\/www.newsbeep.com\/us\/wp-content\/uploads\/2025\/10\/41551_2025_1496_Fig5_HTML.png\" alt=\"figure 5\" loading=\"lazy\" width=\"685\" height=\"636\"\/><\/a><\/p>\n<p>a, An illustration showing example spot patterns with random, clustered and dispersed underlying spatial distributions. b, The equation used here for likelihood calculation. c, An example likelihood plot showing likelihood as a function of radius for random, clustered and dispersed spatial distributions. d, An example of an analysed FOV with an antibody stain for p-syn. e, The same analysed FOV with detected oligomers in blue and red, with red serving to highlight the disease-specific oligomers. f, A plot showing the likelihood of oligomer\u2013oligomer distances, with 95% confidence interval presented as the shaded region, shows that all oligomers tend to spatially cluster, and that disease-specific oligomers have a higher clustering tendency. g\u2013r, Example FOVs stained with antibodies for neurofilaments, P2RY12, GFAP and Olig2 (g, j, m and p), the same images with labelled cells shown in green and disease-specific oligomers highlighted in red (h, k, n and p) and a plot showing the likelihood of oligomer\u2013cell distances, with the 95% confidence interval presented as the shaded region, which shows that disease-specific oligomers tend to cluster in or around neurons, microglia and astrocytes, while being dispersed from oligodendrocyte nuclei (i, l, o and r).<\/p>\n<p>ASA\u2013PD can also be used to interrogate the distance of objects to cell-specific markers in co-stained samples. To do so, we co-stained samples with \u03b1-synuclein and various cell markers, minimizing photobleaching and optimizing the signal of the nanoscale species. We then quantified the density as a function of the proximity to the cell markers (Fig. <a data-track=\"click\" data-track-label=\"link\" data-track-action=\"figure anchor\" href=\"http:\/\/www.nature.com\/articles\/s41551-025-01496-4#Fig5\" rel=\"nofollow noopener\" target=\"_blank\">5g\u2013r<\/a>). For some cell types, namely neurofilament (neurons), P2RY12 (microglia) and GFAP (astrocytes), the disease-specific species showed an increased probability of being localized in proximity to neurofilament (neurons), P2RY12 (microglia) and GFAP (astrocytes). By contrast, disease specific species have a low probability of being localized to the Olig2 marker (oligodendrocyte nuclei). This approach can thus enable quantitative statistical analysis of differences of disease-specific species density over large data sets.<\/p>\n","protected":false},"excerpt":{"rendered":"Autofluorescence suppression and high-sensitivity microscopy reveals nanoscale assemblies in human brain tissue An overview of the ASA\u2013PD pipeline&hellip;\n","protected":false},"author":2,"featured_media":195487,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[34],"tags":[97155,258,257,97,36501,113252],"class_list":{"0":"post-195486","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-health","8":"tag-biomedical-engineering-biotechnology","9":"tag-biomedicine","10":"tag-general","11":"tag-health","12":"tag-high-throughput-screening","13":"tag-nanoscale-biophysics"},"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/posts\/195486","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/comments?post=195486"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/posts\/195486\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/media\/195487"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/media?parent=195486"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/categories?post=195486"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/tags?post=195486"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}