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Mirzaei"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"disease":["Age Related Macular Degeneration"],"software":["Not available"],"submitter_keywords":["single-cell rna sequencing","proteomics.","Human induced pluripotent stem cells","transcriptomics","retinal pigment epithelium","reticular pseudodrusen","age-related macular degeneration","Human induced pluripotent stem cells; retinal pigment epithelium; single-cell rna sequencing; genome regulation; age-related macular degeneration; reticular pseudodrusen; transcriptomics; proteomics.","genome regulation"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD070797"],"tissue":["Pluripotent Stem Cell","Cell Culture"],"sample_protocol":["RPE cell cultures were lysed in RIPA buffer containing phosphatase and protease inhibitors, then sonicated (40 Hz, 2 pulses of 15 s each) using a probe sonicator. Insoluble debris was removed by centrifugation at 14,000 rpm for 15 minutes at 4°C. Protein concentrations were measured using the bicinchoninic acid (BCA) protein assay kit (Thermo Scientific). Extracted proteins (50 μg) were adjusted to 50 μL in 1× S-Trap lysis buffer and reduced/alkylated with TCEP and MMTS. The S-Trap midi protocol (Protifi) was performed. Phosphoric acid was added to the SDS lysate (final concentration 1.2%), followed by the addition of 350 μL S-Trap binding buffer (90% aqueous methanol with 100 mM TEAB). The mixture was loaded onto an S-Trap column, washed, and digested with trypsin at a 10:1 protein ratio in 50 mM TEAB. After overnight incubation at 37°C, peptides were eluted in three stages, pooled, and concentrated using a Speed-Vac to near dryness (~5 μL remaining).  TMT Labelling and Peptide Fractionation Proteome profiling was conducted on a Tandem Mass Tag (TMT) platform with six independent 16-plex TMT experiments. Dried peptides were resuspended in 100 mM HEPES buffer (pH 8.2), and concentrations were determined with the MicroBCA kit. Peptides from each sample (35 μg) were labelled with 0.2 mg TMT reagent per tube for 1 hour at room temperature with vortexing. Residual TMT reagent was quenched with 8 μL of 5% hydroxylamine. For each 16-plex experiment, labelled samples were combined and dried by vacuum centrifugation. The peptides were cleaned using a C18 column (Sep-pak, Waters) before undergoing high-pH reversed-phase fractionation on an Agilent 1260 HPLC system. Peptides were separated using a 55-minute gradient from 3-30% acetonitrile in 5 mM ammonia (pH 10.5) at a flow rate of 0.3 mL/min. The collected 96 fractions were consolidated into eight final fractions. These were dried, resuspended in 1% formic acid, and desalted using SDB-RPS stage tips.  Liquid Chromatography and Tandem Mass Spectrometry Mass spectrometric data were acquired using an Orbitrap Eclipse mass spectrometer connected to a Vanquish Neo UHPLC system. Approximately 1 µg of peptide was separated on a 100 µm capillary column packed with 35 cm of Accucore 150 resin (2.6 μm, 150Å; ThermoFisher Scientific) at a flow rate of 350 nL/min. The scan sequence started with an MS1 spectrum (Orbitrap analysis, resolution set to 60,000, mass range 350-1350 Th, automatic gain control (AGC) target set to 100%, maximum injection time set to “auto”. Data acquisition lasted 75 minutes per fraction. The high-resolution MS2 (hrMS2) stage involved fragmentation via higher-energy collisional dissociation (HCD) at a normalized collision energy of 36%. Analysis was performed using the Orbitrap (AGC target 200%, maximum injection time 86 ms, isolation window 0.5 Th, resolution 30,000, with TurboTMT enabled). The FAIMSpro interface was used, with a dispersion voltage (DV) of 5,000V and compensation voltages (CVs) set at +30V, -50V, and -70V. The TopSpeed parameter was set to 1 second per CV."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Spectra were converted to mzXML format using MSconvert [100]. Database searches were conducted using all entries from the homo sapiens UniProt reference database (downloaded: June 2024) and a reversed concatenated sequence database. Searches were performed using a 50-ppm precursor ion tolerance for protein profiling and a product ion tolerance of 0.03 Da, maximizing sensitivity for Comet searches and linear discriminant analysis [101,102]. Static modifications included TMTpro labels on lysine residues and peptide N-termini (+304.207 Da), along with carbamidomethylation of cysteine residues (+57.021 Da). Oxidation of methionine residues (+15.995 Da) was set as a variable modification. Peptide-spectrum matches (PSMs) were adjusted to a 1% false discovery rate [103,104]. PSM filtering utilized linear discriminant analysis [102,104], and proteins were assembled to a final protein-level false discovery rate of 1% [104]. Protein quantification was based on summing reporter ion counts from all matching PSMs [105]. Reporter ion intensities were corrected for isotopic impurities according to manufacturer specifications. The signal-to-noise (S/N) measurements for peptides assigned to each protein were summed, and these values were normalized to ensure equal protein loading across channels. Each protein abundance was then scaled such that the summed signal-to-noise ratio for that protein across all channels equaled 100, resulting in a relative abundance (RA) measurement. DEPs were identified through Student’s t-tests, specifically comparing the ratios between both groups. The overall fold changes were calculated as geometric means of the corresponding ratios. For a protein to be considered differentially expressed, we followed the following two criteria: a ratio fold change exceeding 1.2 for upregulated or falling below 0.83 for downregulated expression, and a p value cutoff (t-test p < 0.05). Investigation of protein–protein interactions and functional enrichment gene ontology (GO) analysis of differentially expressed proteins (DEPs) were performed with the online STRING database version 12.0119. STRING analysis on the 715 DEPs within the proteomics dataset, generated a network of interactions (based on both evidence of functional and physical interactions). The top hits were selected based on the minimum required interaction score of 0.9 (highest confidence), and the full STRING network was deployed to visualise network maps and interactors. Network lines represent the protein interaction score, which was set at a minimum high confidence (0.7) for visualisation. Active interaction sources were based on text mining, experiments, databases, coexpression, neighbourhood, gene fusion, and co-occurrence data. The network analysis uses a strength score of each STRING network, which is the ratio between the number of proteins in the specified network that are annotated with a term, and the number of proteins that STRING expects to be annotated with this term in a random network of the same size (Log10(observed/expected)=strength)."],"omics_type":["Proteomics"],"labhead":["Alice Pebay"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Dame Kate Campbell Fellow  Department of Surgery| Melbourne Medical School  Department of Anatomy and Physiology| School of Biomedical Sciences  Faculty of Medicine, Dentistry and Health Sciences  Medical Building (#181), Grattan Street  The University of Melbourne, Victoria 3010 Australia  P: +61 3 9035 5464 E: apebay@unimelb.edu.au  W: https://medicine.unimelb.edu.au/school-structure/surgery  W: https://biomedicalsciences.unimelb.edu.au/departments/anatomy-and-physiology"],"species":["Homo Sapiens (human)"],"publication":["42106786 Hall JC, Krishna Sudhakar K, Daniszewski M, Senabouth A, Abbott CJ, Liang HH, Kumar H, Lidgerwood GE, Mirzaei M, Ma JY, Atkeson T, Hirokawa Y, Nandrot EF, Barnett A, Cazevieille C, Manes G, Mountford S, Thompson P, Fletcher EL, Wu Z, Bahlo M, Ansell BRE, Paull D, Hewitt AW, Guymer RH, Powell JE, Pébay A. Patient induced pluripotent stem cells identify specificities of a reticular pseudodrusen phenotype in age-related macular degeneration. Genome Med. 2026 18(1):54 10.1186/s13073-026-01658-2"],"submitter_mail":["mehdi.mirzaei@mq.edu.au"],"submitter_affiliation":["macquarie university"],"submitter_country":["Australia"],"pubmed_abstract":["BACKGROUND: Age-related macular degeneration (AMD) is a leading cause of vision loss. Reticular pseudodrusen (RPD), deposits on the apical side of the retinal pigment epithelium (RPE), signify a distinctive and critical AMD phenotype. Yet, their molecular basis and relationship to the conventional drusen seen in AMD remain unclear. METHODS: We generated induced pluripotent stem cell-derived RPE cells from a clinically phenotyped cohort comprising only individuals with conventional drusen (AMD/RPD-) or with drusen coexisting with RPD (AMD/RPD +). To identify differences between the two cohorts, we performed single-cell transcriptomic, proteomic, quantitative trait locus (QTL) and transcriptome-wide association (TWAS) analyses, together with functional assays. RESULTS: AMD/RPD + RPE cells exhibited enrichment of extracellular matrix (ECM) and hypoxia-responsive pathways, and a relative underrepresentation of mitochondrial and oxidative phosphorylation processes, when compared with AMD/RPD- cells. Genetic analyses supported shared modulation of mitochondrial pathways across AMD, with additional regulatory signals associated with RPD risk. Functionally, all RPE cohorts formed drusen-like deposits in vitro. AMD/RPD- lines generated more basal deposits, whereas AMD/RPD + cells exhibited increased susceptibility to monolayer disruption. CONCLUSIONS: These findings indicate that AMD with and without RPD represent mechanistically distinct entities and provide novel insight into the molecular mechanisms underlying disease heterogeneity in AMD."],"pubmed_title":["Patient induced pluripotent stem cells identify specificities of a reticular pseudodrusen phenotype in age-related macular degeneration."],"pubmed_authors":["Hall Jenna C JC, Krishna Sudhakar Kavitha K, Daniszewski Maciej M, Senabouth Anne A, Abbott Carla J CJ, Liang Helena H HH, Kumar Himeesh H, Lidgerwood Grace E GE, Mirzaei Mehdi M, Ma Jessica Yw JY, Atkeson Trevor T, Hirokawa Yumiko Y, Nandrot Emeline F EF, Barnett Alexander A, Cazevieille Chantal C, Manes Gaël G, Mountford Simon S, Thompson Philip P, Fletcher Erica L EL, Wu Zhichao Z, Bahlo Melanie M, Ansell Brendan R E BRE, Paull Daniel D, Hewitt Alex W AW, Guymer Robyn H RH, Powell Joseph E JE, Pébay Alice A"],"additional_accession":[]},"is_claimable":false,"name":"Patient induced pluripotent stem cells identify specificities of a reticular pseudodrusen phenotype in age-related macular degeneration","description":"Age-related macular degeneration (AMD) is a leading cause of vision loss. Reticular pseudodrusen (RPD), deposits on the apical side of the retinal pigment epithelium (RPE), signify a distinctive and critical AMD phenotype. Yet, their molecular basis and relationship to the conventional drusen seen in AMD remain unclear. We generated induced pluripotent stem cell-derived RPE cells from a clinically phenotyped cohort comprising only individuals with conventional drusen (AMD/RPD-) or drusen coexisting with RPD (AMD/RPD+). From these cells, we generated single-cell transcriptomics, proteomics, and functional data to identify differences between the two cohorts. We show that AMD/RPD+ RPE cells exhibit enrichment in extracellular matrix (ECM) remodelling, cytoskeletal, and hypoxia-responsive programs, whereas AMD/RPD- RPE cells display a relatively greater representation of mitochondrial and protein homeostasis pathways. Both subtypes demonstrated molecular hallmarks of ageing, including altered ECM regulation and mitochondrial decline, but differed in the direction and extent of pathway disruption. Expression and protein quantitative trait loci (QTLs) highlight shared genetic influences on mitochondrial and iron-handling pathways, while disease-interacting eQTLs and transcriptome-wide association study identify regulatory signals that are distinctive of the RPD subtype within AMD, including through regulation of ECM. Functionally, all iPSC-derived RPE formed drusen-like deposits in vitro: AMD/RPD- lines generated more basal deposits, whereas AMD/RPD+ cells exhibited greater structural instability under bisretinoid-induced stress. Together, these findings indicate that AMD with and without RPD represent mechanistically distinct entities and provide novel insight into the molecular mechanisms underlying disease heterogeneity in AMD.","dates":{"publication":"2026-06-08","submission":"2025-11-17"},"accession":"PXD070797","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:1589","NEWT:135622","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:8655","NEWT:5147","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:214053","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:90690","NEWT:1436183","NEWT:4232","NEWT:416348","NEWT:11298","NEWT:4236","NEWT:7742","NEWT:196627","NEWT:200308","NEWT:200302","NEWT:870435","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:2666255","NEWT:999810","NCBITaxon:5693","NEWT:28995","NEWT:1392998","NEWT:380394","NEWT:226900","NEWT:1266738","NEWT:231490","NEWT:244704","NEWT:7725","NEWT:9909","NEWT:9902","NEWT:430615","NEWT:72664","NEWT:563041","NEWT:36599","NEWT:41949","NEWT:326423","NEWT:452467","NEWT:198822","NEWT:36111","NEWT:326424","NEWT:1678078","NEWT:749906","NEWT:418985","NEWT:749907","NEWT:150847","NEWT:431947","NE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