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Additional file 6: Table S5. Description of the participants in EMIF-AD MBD cohort.

Additional file 4: Fig. S1. Comparison of the CSF proteomes of the two App knock-in models reveals alterations in ECM proteins. a Volcano plots displaying the changes in protein levels in CSF from AppNL-F/NL-F vs AppNL-G-F/NL-G-F mice. Dash line: p = 0.05. b Heatmap of significantly (p < 0.05) altered proteins in AppNL-F/NL-F mice as compared to AppNL-G-F/NL-G-F mice. Proteins were sorted into upregulated and downregulated proteins in the AppNL-G-F/NL-G-F mice and by significance from highest to lowest (top to bottom).

Additional file 11: Fig. S4. CSF-decorin levels correlates with Aβ pathology in the brains of AppNL-F/NL-F mice. a Spearman’s correlation analysis of parameters related to Aβ plaque load and decorin levels between 12 months old AppNL-F/NL-F and Appwt/wt mice, b AppNL-G-F/NL-G-F and Appwt/wt mice. The corresponding figures for each parameter are denoted. The correlation coefficients are displayed (*p < 0.05, **p < 0.01, ***p < 0.001). The red color represents positive correlation, and the green color represents negative correlation according to the scale bars in the right column.

Additional file 3: Table S3. Significantly altered ECM associated proteins in mouse CSF identified by MS and PEA.

Additional file 9: Fig. S2. CSF-decorin negatively correlates with CSF-t-tau and CSF-p-tau in the whole EMIF-AD MBD cohort. a Correlations of CSF-DCN and CSF-Aβ42, b CSF-DCN and CSF-t-tau, c CSF-DCN and CSF-p-tau in the whole EMIF-AD MBD cohort (n = 310), including NC (n = 139), MCI (n = 92) and AD (n = 79) were analyzed. The regression coefficients (Beta) and p-values are displayed. DCN decorin.

Additional file 2. Proximity ligation assay showing co-localization of ADAM0 and BACE1 with their substrate APP in human post mortem AD and control brain hippocampus. Human control (ctrl) (a, c and e) and AD (b, d and f) hippocampal sections were subjected to PLA and each signal (brown dot) generated denotes two proteins within 40 nm distance from each other. (a–b) APP and ADAM10, (c–d) APP and BACE1. Primary antibodies were excluded from the negative control (e–f) sections. Brain tissue and cell nuclei were visualized by a nuclear stain solution containing Mayer´s haematoxylin. Each experiment was performed three times and representative images are shown. Scale bar 20 µm.

Additional file 1. Proximity ligation assay showing co-localization of ADAM10 and BACE1 with their substrate APP in adult rat brain. Adult rat brain hippocampal sections were subjected to PLA and each signal (brown dot) generated denotes two proteins within 40 nm distance from each other. (a) APP and ADAM10, (b) APP and BACE1. (c) Negative control with no primary antibodies. Brain tissue and cell nuclei were visualized by a nuclear stain solution containing Mayer´s haematoxylin. Each experiment was performed three times and representative images are shown. Scale bar 20 µm.

Synaptic dysfunction is an early pathogenic event in Alzheimer disease (AD). Hence the maintenance of healthy neurotransmission becomes crucial to slow or halt cognitive decline. In search of identifying proteins that could play a role in synaptic dysfunction, we studied the proteome of a highly vulnerable hippocampal region that is enriched in excitatory synapses. Our in-depth proteomic analysis suggests an impaired presynaptic signaling in AD. Using immunohistochemistry, we verified significantly reduced levels of complexin-1, complexin-2, and synaptogyrin-1 in AD., Graphical Abstract Highlights Laser microdissection of highly vulnerable hippocampal region. Proteomic analysis of postmortem human brain tissue of AD and control cases. Decreased levels of presynaptic proteins, but not postsynaptic proteins, in AD. Immunohistochemistry verifies decreased levels of selected presynaptic proteins., Synaptic dysfunction is an early pathogenic event in Alzheimer disease (AD) that contributes to network disturbances and cognitive decline. Some synapses are more vulnerable than others, including the synapses of the perforant path, which provides the main excitatory input to the hippocampus. To elucidate the molecular mechanisms underlying the dysfunction of these synapses, we performed an explorative proteomic study of the dentate terminal zone of the perforant path. The outer two-thirds of the molecular layer of the dentate gyrus, where the perforant path synapses are located, was microdissected from five subjects with AD and five controls. The microdissected tissues were dissolved and digested by trypsin. Peptides from each sample were labeled with different isobaric tags, pooled together and pre-fractionated into 72 fractions by high-resolution isoelectric focusing. Each fraction was then analyzed by liquid chromatography-mass spectrometry. We quantified the relative expression levels of 7322 proteins, whereof 724 showed significantly altered levels in AD. Our comprehensive data analysis using enrichment and pathway analyses strongly indicated that presynaptic signaling, such as exocytosis and synaptic vesicle cycle processes, is severely disturbed in this area in AD, whereas postsynaptic proteins remained unchanged. Among the significantly altered proteins, we selected three of the most downregulated synaptic proteins; complexin-1, complexin-2 and synaptogyrin-1, for further validation, using a new cohort consisting of six AD and eight control cases. Semi-quantitative analysis of immunohistochemical staining confirmed decreased levels of complexin-1, complexin-2 and synaptogyrin-1 in the outer two-thirds of the molecular layer of the dentate gyrus in AD. Our in-depth proteomic analysis provides extensive knowledge on the potential molecular mechanism underlying synaptic dysfunction related to AD and supports that presynaptic alterations are more important than postsynaptic changes in early stages of the disease. The specific synaptic proteins identified could potentially be targeted to halt synaptic dysfunction in AD.

Figure S1. MAO-B antibody validation, precipitation and expression experiments. Figure S2. Western blot (WB) of postmortem AD and control human brain homogenate with MAO-B antibody. Figure S3. Validation of the Aβ42-specific antibody G2-11 by immunocytochemistry. Figure S4. MAO-B and Ab42 quantification in single cells from MAO-B silenced cortex neurons. Figure S5. Treatment of primary cortical neurons with fluorescently labeled siRNA. (PDF 1472 kb)