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Santiago"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"disease":["Alzheimer's Disease"],"software":[""],"submitter_keywords":["Human","Retina","Alzheimer's"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073336"],"tissue":["Brain","Retina"],"sample_protocol":["At autopsy, the lenses of the right eyes were removed, filled with O.C.T. mounting medium (Vector Laboratories), and subsequently frozen for storage at -80 °C. Each eyeball was cut into eight clefts, leaving a 0.5 cm margin around the optic nerve intact. Retinal tissue was collected from the nasal superior region for this study. Hippocampal tissue was snap-frozen at autopsy in 1 cm-thick sections and stored at -80 °C. For analysis, the tissue was further sectioned into 0.5 cm-thick slices. A 3 mm biopsy punch (Kai Medical) was used to dissect samples from the Cornu Ammonis 1 (CA1) region adjacent to the subiculum. The CA1 was selected due to its early involvement in AD pathology (3, 46). Both retinal and hippocampal samples were transferred to 1.5 mL Pink Rino Tubes with screw caps, and 100 µL of Lysis buffer (50 mM Tris-HCl pH 7.5, 50 mM NaCl, 1 mM EDTA, 5 mM NaH₂PO₄, 1 mM DTT, 0.1% phosphatase 1, 0.03% phosphatase 2, 0.05% protease inhibitors; Sigma-Aldrich) was added. Samples were homogenized in a Bullet Blender Storm Pro (BT24M, Next Advance, Inc., Troy, NY, USA) at speed 8 for 3 min, followed by centrifugation at 14,000 × g for 10 min. Supernatants were collected into new Eppendorf tubes. The residual material was washed with 50 µL Lysis buffer, centrifuged again, and the supernatant pooled with the previous fraction. The remaining tissue in the Rino tubes underwent a second extraction using RIPA buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) and supernatants were collected in new Eppendorf tubes.  This two-step protocol was designed to capture proteins with different biochemical properties and solubilities. The Lysis buffer uses mild ionic conditions without detergents, extracting soluble cytoplasmic proteins and loosely membrane-associated proteins while mostly preserving cellular structures. The subsequent RIPA buffer employs both ionic and non-ionic detergents (Triton X-100 and sodium deoxycholate) under higher ionic strength, enabling extraction of proteins from disrupted membranes, protein complexes, and cellular compartments resistant to mild lysis. This sequential approach allows detection of proteins that might exist in different biochemical states (e.g., soluble vs. complex-bound) or subcellular localizations between disease and control tissues, providing complementary views of the proteome that would not be captured by a single extraction method. For downstream processing, 50 µL of each sample was reduced with DTT (final 10 mM) at 56 °C for 30 min, followed by alkylation with iodoacetamide (final 20 mM) for 30 min in the dark. Proteins were precipitated with ice-cold ethanol (final 90%) overnight at −20 °C and pelleted by centrifugation at 14,000 × g for 10 min. Pellets were air-dried and resuspended in 50 µL 100 mM ammonium bicarbonate, then disrupted using a BioRuptor (Diagenode Inc., Denville, USA) for 20 cycles of 15 s on/off. Samples were centrifuged at 14,000 × g for 10 min, and the supernatant transferred to new tubes. Protein concentration was determined using a NanoDrop (DeNovix, AH Diagnostics) at A₂₈₀ nm. For digestion, 15 µg of protein per sample was incubated with trypsin (Promega, Madison, WI) at a 1:50 enzyme: protein ratio overnight at 37 °C. Digestion was stopped by adding 5 µL of 10% trifluoroacetic acid (TFA). Samples were dried in a SpeedVac and resuspended in 22 µL of 2% acetonitrile/0.1% TFA for mass spectrometry analysis.Peptide separation and mass spectrometry: For analysis, 2 µL of each sample was injected into an Exploris 480 mass spectrometer (Thermo Fisher Scientific) coupled to a Vanquish Neo UHPLC system (Thermo Fisher Scientific). Peptides were first loaded onto an Acclaim PepMap 100 C18 precolumn (75 µm × 2 cm, Thermo Scientific) and then separated on an EASY-Spray C18 column (75 µm × 25 cm, 2 µm, 100 Å, ES902) at a flow rate of 300 nL/min and a column temperature of 45 °C. A 120 min nonlinear gradient was applied using Solvent A (0.1% FA in water) and Solvent B (0.1% FA in 80% ACN): 5–25% B over 100 min, 25–32% B over 12 min, and 32–45% B over 8 min. Mass spectrometry acquisition: Data were acquired in data-dependent acquisition (DDA) mode in positive polarity. Full MS1 scans were acquired at a resolution of 120,000 (m/z 200), with a normalized AGC target of 300% and a maximum injection time of 45 ms over a mass range of 350–1400 m/z. Precursors were isolated using a 1.3 m/z window and fragmented by HCD with a normalized collision energy of 30. MS2 spectra were recorded in the Orbitrap at a resolution of 15,000, with a normalized AGC target of 100% and custom maximum injection time. An intensity threshold of 10⁴ and dynamic exclusion of 60 s were applied."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Raw spectra were processed using Proteome Discoverer 2.5 (Thermo Fisher Scientific) and searched against the UniProt Human canonical database (UP000005640) for protein identification and label-free quantification across retinal and hippocampal tissues. Precursor and fragment tolerances were set to 10 ppm and 0.02 Da, respectively. Trypsin was specified as the protease, with methionine oxidation, asparagine deamidation, phosphorylation, general oxidation, and protein N-terminal acetylation set as variable modifications, and cysteine carbamidomethylation as a fixed modification. Label-free quantification was performed using peptide peak intensities extracted from Proteome Discoverer. Statistical analysis, enrichment and cell-type mapping Label-free protein intensities (obtained via Proteome Discoverer 2.5) were first filtered to retain proteins identified at ≤1% FDR, supported by at least two unique peptides, and detected in a minimum of 70% of samples. After log₂ transformation and median normalization per sample (row-wise), missing values were imputed using a left-shifted, normal distribution (shifted 2 SD below the protein’s mean log-intensity, with a width of 0.3×SD, capped at the lowest observed value). This models undetected low-abundance signals and is standard for Missing-Not-At-Random (MNAR) imputation in label-free proteomics (47, 48). Differential abundance between AD and NC samples was assessed separately in the retina and hippocampus using linear mixedeffects modeling (via statsmodels MixedLM). The fixedeffects structure was specified as: Protein ~ C(Buffer) * C(Diagnosis) + C(Sex) + Age + (1∣Subject) where Buffer denotes the extraction method (Lysis or RIPA), Diagnosis indicates AD versus NC, Sex and Age were included as covariates to control for demographic differences, and Subject identity was modeled as a random intercept to account for paired measures (both buffers from the same donor). For both tissues, the primary focus was on the main effect of Diagnosis; the Buffer × Diagnosis interaction was evaluated as a secondary outcome to explore potential extractionmethod specific differentials. Regression coefficients (β) and false discovery rate (FDR)adjusted pvalues were reported per protein. Proteins meeting FDR < 0.05 were designated differentially abundant proteins (DAPs). Intersection of DAPs between retina and hippocampus was identified for downstream comparative analyses. Partial Spearman correlation analyses (adjusted for age and sex) were conducted to examine disease-related associations. First, correlations were computed between each of the top 20 up- and down-regulated retinal proteins and stages of Alzheimer’s pathology, neurofibrillary tangle (NFT) and amyloid β (Aβ) plaque burden. Second, proteins that were differentially abundant in both retina and brain and exhibited changes in the same direction were correlated between tissues to identify shared molecular alterations. Third, retinal values of those proteins showing significant retina-brain correlations were further correlated with retinal phosphorylated tau (p-tau) values at sites previously reported to be altered in the presence of AD pathology in our earlier study(41). Functional enrichment of differentially abundant proteins (DAPs) was performed using g:Profiler, examining Gene Ontology (BP, MF, CC), and Reactome pathways. Analyses were conducted using two complementary background sets: (i) the full proteome detected in the experiment, to account for proteins actually measured, and (ii) the Human Protein Atlas of proteins in the retina or hippocampus, to provide a broader reference of human proteins. Using both backgrounds ensures robust enrichment results while mitigating potential biases from incomplete experimental detection. Terms with FDR < 0.05 were considered significant. All normalization, statistical analyses, and data visualizations described above were performed using Python (version 3.13.1). DAPs were mapped to retinal cell types using single-cell reference data from the Human Cell Atlas Retina v1.0 and visualized via the Cell x Gene Discover platform (49, 50). DAPs were first converted to gene symbols and plotted to display their combined expression across all cells in a UMAP embedding of annotated retinal populations. Individual highly changed DAPs were also visualized individually to show their expression patterns across specific cell types."],"omics_type":["Proteomics"],"labhead":["Malin Wennström"],"instrument_platform":[""],"labhead_affiliation":["Cognitive Disorder Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["jessica.dos_reis_santiago@med.lu.se"],"publication":["10.1007/S00401-026-03054-X","10.1007/s00401-026-03054-x"],"submitter_affiliation":["Lund University"],"submitter_country":["Sweden"],"additional_accession":[]},"is_claimable":false,"name":"Retinal proteome changes mirror brain pathology and reveal synaptic and cytoskeletal dysfunction in Alzheimer’s disease","description":"Visual dysfunction is increasingly recognized as an important feature of Alzheimer’s disease, and substantial retinal changes have been documented across multiple studies. Yet the molecular changes underlying retinal neurodegeneration and which retinal protein signatures best track cerebral pathology remain incompletely defined. Here, we performed comprehensive mass spectrometry-based proteomics on paired retinal and hippocampal tissue from the same postmortem donors (8 AD, 8 non-demented controls) to identify disease-associated molecular signatures and assess their overlap between these tissues. Using a sequential dual-extraction protocol,  differentially abundant proteins (DAPs) were identified with mixed-effects modeling. Functional enrichment and cell-type mapping based on single-cell retinal reference data assessed pathway alterations and cellular distribution of disease-associated proteins.","dates":{"publication":"2026-07-29","submission":"2026-01-21"},"accession":"PXD073336","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:1247","NEWT:376741","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:5821","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:28909","NEWT:515849","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:143361","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:747078","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:294381","NEWT:197","NEWT:1390363","NEWT:77133","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:498217","NEWT:156471","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:156476","NEWT:286","NEWT:391619","NEWT:360104","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:1143","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:172","NEWT:296543","NEWT:316435","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:105023","NEWT:866628","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:2850","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:269796","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:9483","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:109757","NEWT:943146","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:180923","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:118499","NEWT:169963","NEWT:32644","NEWT:527796","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:375451","NEWT:352472","NEWT:357","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:1328426","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:327159","NEWT:178876","NEWT:1660","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:7237","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1821314","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:5286","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:9644","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:27592","NEWT:98334","NEWT:426428","NEWT:63459","NEWT:1276815","NEWT:36185","NEWT:588858","NEWT:9639","NCBITaxon:11071","NEWT:242231","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:929793","N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