Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/SDRF.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA002_A375_NLS-mT-2hB_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA001_A375_NLS-mT-2hB_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA007_A375_hSOX10-mT-2hB_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA003_PostBlank_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA004_A375_mT-hSOX10-2hB_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA006_PostBlank_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA005_A375_mT-hSOX10-2hB_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA008_A375_hSOX10-mT-2hB_2_Rerun.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA003_A375_NLS-mT-2hB_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA009_A375_hSOX10-mT-2hB_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA009_PostBlank_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/KA006_A375_mT-hSOX10-2hB_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/mT_and_contaminant_FASTA_20240208.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/Human_SwissprotReviewed_2024_02_08_UP000005640.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD067868/MQSearch.zipprimaryOK200ckkaufman@wustl.eduDhaval BhattData-dependent acquisitionAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryBottom-up proteomicsMelanomaMiniturboHsox10MelanomaInteractome mappingMass spectrometryProximity-based biotinylationProtein-protein interactionshttps://www.ebi.ac.uk/pride/archive/projects/PXD067868MelanocyteSkinProtein biotinylation and extraction A375 cells stably expressing hSOX10-mT, mT-hSOX10, or NLS-mT control constructs were plated in 15-cm dishes and grown to 85–90% confluence. For each construct, three biological replicates (seven plates per replicate) were used. To induce biotinylation, cells were treated with 50 μM exogenous biotin in DMEM supplemented with 10% FBS and 1 μg/mL puromycin for 90 minutes at 37°C. Following treatment, the media was discarded, and cells were washed twice with 10 mL of ice-cold PBS per plate. After rinses, cells were scraped on ice into 5 mL of PBS per plate and pooled into pre-chilled 50-mL conical tubes. Residual cells were collected by washing all plates with an additional 10 mL of PBS. For each biological replicate, the pooled cells from seven plates were combined into a single tube, resulting in nine tubes total (three replicates for each construct). The pooled cells were centrifuged at 500xg for 10 minutes at 4°C, and the supernatant was discarded. Cell pellets were resuspended in RIPA lysis buffer (50 mM HEPES pH 8, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.2% sodium deoxycholate, and 10% glycerol) supplemented with 1X Halt protease inhibitor cocktail (100X; Thermo Scientific, 1861279), 1X NEM (freshly prepared from a 1M ethanol stock; 100X; Thermo Scientific, 23030), and benzonase (1:5000 dilution; Sigma, E1014-25KU). Each tube of cell pellets (representing one biological replicate) resuspended in RIPA lysis buffer was passed through a 21-gauge needle five times to shear membranes and ensure complete lysis. Lysates were then rocked at 4°C for 15 minutes and centrifuged at 20,000xg for 5 minutes at 4°C to pellet debris. Clarified supernatants were transferred to pre-chilled tubes and stored at −80°C. Streptavidin pull-down Protein concentrations were determined using the Pierce BCA Protein Assay Kit according to the manufacturer’s instructions. For each biological replicate, 20 mg of total protein was prepared in a final volume of 8 mL RIPA lysis buffer. Streptavidin-conjugated Sepharose beads (Cytiva, GE17-5113-01) were pre-washed in RIPA lysis buffer three times and centrifuged at 400xg for 2 minutes at 4°C after each wash. After washing, 30 μL of pre-washed beads was added to the protein lysates for each sample. The lysates were incubated with beads overnight at 4°C with gentle rotation to bind biotinylated proteins. Following incubation, the beads were pelleted by centrifugation at 400xg for 2 minutes at 4°C, and the unbound supernatant was discarded. The beads were washed sequentially with 1 mL wash buffers with increasingly stringency to remove non-specific binders. The washes included two rounds with 2% SDS in water (WB1), one round with a high-salt buffer (500 mM NaCl, 0.1% deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5; WB2), one round with a lithium chloride buffer (250 mM LiCl, 0.5% Triton X-100, 0.5% deoxycholate, 1 mM EDTA, 50 mM HEPES pH 8.1; WB3), one round with a low-salt buffer (150 mM NaCl, 50 mM HEPES pH 7.4; WB4), and three rounds with 50 mM ammonium bicarbonate (ABC buffer; WB5). After each wash, the beads were resuspended, inverted gently 10 times, and centrifuged at 400xg for 2 minutes at room temperature. Beads were stored at 4°C or immediately processed for downstream analyses. Sample preparation for mass spectrometry analyses After washing, bound proteins on streptavidin beads were digested by resuspending in 100 μL of 50 mM ammonium bicarbonate (ABC) and overnight incubation at 37°C with 1 μg of a trypsin (Promega V5113) mixed with 0.5 mAU of Lys-C (Wako Chemicals, 129-02541). An additional 0.5 μg of trypsin/Lys-C was added the next day, and digestion continued for 2 hours. Peptides were collected by centrifugation, pooled with washes from the beads, and passed through BioPureSPN columns (Nest Group, 10 µm frit, C100500) pre-washed with 50 mM ABC. Filtered peptides were acidified to 2% formic acid (FA) and dried in a SpeedVac. Dried peptides were resuspended in 25 μL of 0.1% FA and 2% acetonitrile in water. Peptide concentrations were measured with a fluorometric BCA assay, and samples were normalized to 1 μg of peptide per 10 μL injection volume. Final samples were transferred to autosampler vials for mass spectrometry.PrideMaxQuant data search All raw mass spectrometry data files were analyzed for protein identification and label-free quantification (LFQ) using MaxQuant (version 2.5.1.0) (Tyanova S et al., 2016a) using the default settings for “Orbitrap” instruments with minor modifications. The datasets for the N- and C-terminal mT-tagged hSOX10 experiments and the nuclear localized mT biotin ligase control were searched against the human UniProt reference proteome database (UP000005640_9606, updated 2024-02-08, https://www.uniprot.org/proteomes/UP000005640) plus a list of likely contaminants containing streptavidin, Trypsin, Albumin, mT (with different subcellular localizations), and against the contaminants list of MaxQuant. The search parameters were as follows: Methionine oxidation (+15.994914 Da) and protein N-terminal acetylation (+42.010564 Da) were set as variable modifications with a maximum of five modifications per peptide. Digestion was set to Trypsin/P with a maximum of four missed cleavages, and a minimum allowed peptide length of seven. Both unique and razor peptides were used for protein quantification, and the minimum LFQ ratio count was set to 2. Fast LFQ with classic normalization was active with a minimum and an average number of neighbors of 3 and 6, respectively. Match between runs for samples within a group (with a match time window of 0.4 min and a 20 min alignment time window) and second peptides were enabled. The raw mass spectrometry proteomics data will be deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository. Perseus data analysis Data filtering and statistical analysis for the proximity dataset were done using Perseus (version 2.0.11.0).27 The ‘proteinGroups.txt’ output file from MaxQuant was loaded into Perseus using raw intensities for all samples as the Main columns. The data matrix was filtered to remove all proteins labeled as “Only identified by site”, “Reverse”, and “Potential contaminant”. The intensity values were transformed to log2(x), and the individual columns were grouped by Bait. Proteins without quantified/valid values in all three replicates for at least one the groups were removed. And the remaining missing values were imputed using the “Replace missing values from normal distribution” function with a width of 0.3 and a downshift of 1.8 from the standard deviation for the total matrix. Principal component analysis was performed to study the distribution of mT-hSOX10, hSOX10-mT and NLS-mT bait replicates. To identify proteins enriched in mT-hSOX10 and hSOX10-mT groups against the NLS-mT control group, two-sided unpaired Student's t-tests were performed with a permutation-based FDR calculation (250 permutations; FDR = 0.05). Volcano plots were generated using -Log10 p-value (y-axis) vs. Log2 fold change (x-axis) values. Protein changes were considered significant when the Log2 fold change (hSOX10 vs. NLS) >1.0 or <-1.0 and the adjusted p-value (q-values) <0.05.ProteomicsCharles K. KaufmanDivision of Medical Oncology and Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA. Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.PARTIALHomo Sapiens (human)dhaval.bhatt@wustl.edu42117278 Newsom-Stewart CM, Bhatt DP, Major MB, Kaufman CK. Mapping of the hSOX10 Proximal Protein Interactome in Human Melanoma. J Proteome Res. 2026 25(6):2649-2668 10.1021/acs.jproteome.5c00852Washington University in St. LouisUnited StatesThe transcription factor SOX10 is a central regulator of melanoma, influencing tumor initiation, progression, phenotypic plasticity, and therapeutic resistance, yet the protein-protein interactions underlying its function remain poorly defined. To address this, we conducted the first dedicated, comprehensive mapping of the human SOX10 (hSOX10) proximal protein interactome using miniTurbo (mT) proximity-dependent biotinylation coupled with mass spectrometry in A375 melanoma cells. Stable lines expressing N- or C-terminal mT-tagged hSOX10 fusion proteins at near-endogenous levels enabled the unbiased capture of proximal proteins in a native cellular context, identifying 847 melanoma-enriched candidate hSOX10 interactors. Stringent statistical filtering, contaminant frequency profiling, and subcellular localization context refined this to 180 high-confidence candidates, including known hSOX10 partners and previously unidentified candidates. Integration of orthogonal biological relevance criteria (functional enrichment and network context, transcriptomic coexpression with hSOX10, and genomic co-occurrence in melanoma) further refined the dataset to 124 biologically relevant candidates enriched for transcriptional regulators, cofactors, chromatin-modifying complexes, and associated pathways. These proteins were stratified using an evidence-based prioritization framework incorporating transcriptomic, genomic, and chromatin-based context without additional exclusion. Collectively, this work provides a high-confidence resource for the hSOX10 proximal protein interactome in melanoma and a framework for generating testable hypotheses regarding hSOX10-associated regulatory networks, melanoma biology, and therapeutic vulnerabilities.Mapping of the hSOX10 Proximal Protein Interactome in Human Melanoma.Newsom-Stewart Catherine M CM, Bhatt Dhaval P DP, Major Michael B MB, Kaufman Charles K CKfalseMapping of the hSOX10 protein interactome in human melanomaThe transcription factor SOX10 is a central regulator of melanoma biology, influencing tumor initiation, progression, phenotypic plasticity, and therapeutic resistance. However, the molecular mechanisms underlying these diverse functions remain incompletely understood. To elucidate the protein-protein interactions (PPIs) that mediate SOX10 activity in melanoma, we mapped the human SOX10 (hSOX10) interactome for the first time in human melanoma cells (A375 line). Given the challenges of capturing transient and weak transcription factor interactions, we employed miniTurbo (mT) proximity-dependent biotinylation coupled with mass spectrometry (MS). Stable A375 cell lines expressing N- and C-terminal mT-tagged hSOX10 fusion proteins at physiologically relevant levels were generated, enabling unbiased biotinylation and MS-based identification of candidate interacting proteins. This approach revealed 847 melanoma-enriched candidate interactors, including 213 high-confidence hits. These included both known hSOX10 partners and previously unidentified putative interactors. Functional annotation of our hSOX10 interactome highlighted associations with chromatin remodeling, transcriptional regulation, SUMOylation, and DNA damage response pathways. Western blot validation of select interactors supported the robustness of our dataset. This first comprehensive map of the hSOX10 interactome in melanoma provides a critical foundation for future investigations into SOX10-driven transcriptional networks and their potential as therapeutic targets and biomarkers in melanoma.2026-06-152025-08-29PXD067868NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:10245NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:43186NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:145458NEWT:633149NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:1772NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NEWT:272634NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:118562NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:419610NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCBITaxon:11320NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:452680NEWT:8839NEWT:90690NEWT:1436183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