{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/allPeptides.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/proteinGroups.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/peptides.txt"],"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/mqpar.xml"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/Lara_241129_P3630_JS_RG_Dimethyl_SL3_5of15_R1_20241204031842.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/Lara_241129_P3630_JS_RG_Dimethyl_SL6_5of15_R1_20241204093423.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/Lara_241129_P3630_JS_RG_Dimethyl_SL2_5of15_R1_20241204011328.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/Lara_241129_P3630_JS_RG_Dimethyl_SL5_5of15_R1_20241204072909.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/Lara_241129_P3630_JS_RG_Dimethyl_SL4_5of15_R1_20241204052355.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD065108/Lara_241129_P3630_JS_RG_Dimethyl_SL1_5of15_R1_20241203230806.raw"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["m.luzarowski@zmbh.uni-heidelberg.de"],"submitter":["Marcin Luzarowski"],"technology_type":["Data-dependent acquisition","Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["3d structure","Specific alterations","Snp","Ipsc","Genetic variation","Gene editing","Crispr","Snv","5mc","Epigenetic","Gene expression"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD065108"],"sample_protocol":["Oligonucleotides for affinity purification (Supplementary table 1, column Y) were ordered from Microsynth with a biotin moiety added to the forward primer, suspended (100 μM), and then annealed in a PCR thermocycler ([95 °C, 5 min] × 1; [95 °C, -0.1 °C, 3 s] × 800; 4 °C, hold) to give a final concentration of 25 μM of annealed oligo. Oligos were then diluted in DNA binding buffer (DBB: 1 M NaCl, 10mM Tris (pH 8.0), 1mM EDTA, 0.05% NP-40) to a 2 μM concentration in a 200-μl volume per replicate. Streptavidine-Sepharose bead slurry (20 μl per replicate, Cytiva, 17511301) was washed once with PBS + 0.1% NP-40 (1ml), the beads collected by centrifugation (2000g, 2 min, 4°C), and the supernatant removed. Then, the beads were washed once with DBB, suspended in the same volume DBB, and added to the diluted oligos. Oligos were bound to streptavidin beads for 30 min at 4 °C on a rotating wheel. Samples were then washed once with DBB (1 ml) and twice with protein binding buffer (PBB: 150 mM NaCl, 50 mM Tris, pH 8, 0.25% NP-40, 1 mM Tris(2-carboxyethyl) phosphine (TCEP) and complete protease inhibitor (Roche)). KOLF2.1J cells (100 × 106) were harvested using ReLeSR and nuclei were extracted by suspending in 5 ml of Buffer A (10 mM HEPES (pH 7.9), 10 mM KCl, 10 mM EDTA, 0.5% NP-40, 1 mM DTT and complete protease inhibitor (Roche)) and incubating on ice for 10 min with vortexing at maximum speed every 2 min for 10 s. Nuclei were collected by centrifugation (800g, 10 min, 4 °C), and the supernatant was carefully removed using a vacuum. Nuclei were disrupted in 750 μl Buffer B (20 mM HEPES (pH 7.9), 400 mM NaCl, 1 mM EDTA, 1% glycerol, 1 mM DTT, complete protease inhibitor (Roche)) by pipetting up and down with a 1-ml pipette until it was possible to pipette them up and down with a 200-μl tip, this was done on ice. Disrupted nuclei were placed into a vortex block in a cold room, vortexed at maximum speed for 10 s, and then incubated at mid-speed (around 5) for 2 h at 4 °C, with vortexing at maximum speed for 10 s every half an hour. Samples were centrifuged (800g, 10 min, 4 °C), and the supernatant was collected. The protein quantity was measured by Qbit using Protein BR Assay Kit (Invitrogen, A50668). For each affinity purification (61), KOLF2.1J nuclear extract (150 μg) was diluted in a 500 μl final volume in PBB and added to the oligo-bound streptavidin beads. Samples were incubated for 2 h at 4 °C with slow rotation. Samples were washed four times with washing buffer (150 mM NaCl, 100 mM ammonium bicarbonate) and twice with PBS.  Beads were suspended in elution buffer (50 μl, 2 M Urea, 100 mM Tris (pH 8.4), 10 mM DTT) and incubated for 20 min at room temperature with agitation (1250 rpm), then frozen at -20 °C ready for mass spectrometry analysis. Following the affinity purification, IAA was added (50 mM) and incubated in the dark at room temperature with agitation (10 min, 1250 rpm). Proteins were digested with Trypsin (150 ng, Thermofisher) and LysC (100 ng, Wako Chemicals) at RT with agitation (2 h, 1250 rpm). Beads were collected by centrifugation (2000g, 2 min), and the supernatant was transferred to a LowBind tube. Beads were suspended in elution buffer (50 μl), incubated at room temperature with agitation (5 min, 1250 rpm), collected (2000g, 2 min), and the supernatant added to the LowBind tube.  Trypsin (100 ng) was added and cleaved overnight with intermittent agitation (37 °C, 1250 rpm for 5 min per hour). The generated peptides were acidified with 1 μl of 20% TFA and light and medium dimethyl labeling was done to allow to combine the wild-type allele with the alternative allele for simultaneous measurement. The samples were analysed by capillary liquid chromatography tandem mass spectrometry connected to a Orbitrap Fusion (Thermo Fisher Scientific)."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Protein identification and relative quantification of the proteins was done with MaxQuant (version 2.4.9.0). Andromeda search engine was used to search the spectras against the Homo Sapiens UniProt database as reference. Common contaminants and highly abundant background proteins were removed. Protein groups were filtered to keep only ones that were identified with at least two peptides, as well as the ones with one or more unique peptides. Protein intensities were log₂-transformed, and variability across replicates was calculated using the coefficient of variation (CV). Proteins with a CV above 10% were excluded to ensure reproducibility. Subsequently, log2-transformed intensities of light-labelled (A|A) samples were compared to the medium-labelled (G|G) samples. To identify significantly enriched proteins, a two-sample paired t-test was performed, and a minimum log-fold change of 1/-1 was required. Processed mass spec data is in Supplementary table 10."],"omics_type":["Proteomics"],"labhead":["Marcin Luzarowski"],"instrument_platform":[""],"labhead_affiliation":["Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["m.luzarowski@zmbh.uni-heidelberg.de"],"publication":["Not available"],"submitter_affiliation":["University of Heidelberg"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Dissecting genotype-specific effects of disease-associated genetic variants","description":"Background For many complex diseases, including Parkinson’s disease, regulatory elements located in intergenic regions have been putatively associated with disease risk and development. However, the biological mechanisms linking these intergenic loci to disease pathogenesis remain largely unknown. Fundamentally, this is because these intergenic loci are non-coding, and bespoke approaches to in-depth functional characterisation are required. Here we utilised an integrative, functional approach to identify the genotype-specific impacts of Parkinson’s disease-associated variant rs11610045, located within a complex region on chromosome 12.   Methods & Results We utilised CRISPR-Cas9 editing (and reversal) to generate isogenic iPSC clones from the KOLF2.1J line containing either the A|A (WT) or G|G (edited) rs11610045 genotype. We also reverted the G|G genotype back to the A|A genotype in two clones to control for off-target effects. Functional profiling of these clones demonstrated allele-specific regulation of both nearby and distal genes, including THBS1 and PDGFB. Further, affinity purification followed by mass spectrometry identified the differential binding of potential regulatory proteins to the G|G genotype compared to the WT A|A genotype, including the transcription factor TCF7L1.   Conclusions Our findings support a model in which non-coding variants, such as rs11610045, impact the expression and downstream activity of multiple genes predominantly through trans-acting mechanisms. In so doing, this study demonstrates a pipeline to delineate SNP-specific impacts in an iPSC model. Finally, we highlight the challenge of aligning genotype dependent expectations of the impact of expression quantitative loci on genes as part of the exploration of how inherited genetic variation contributes to complex genetic 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