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Province"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Quantitative proteomics","Familial adenomatous polyposis","Mucosa","Tandem mass tag","Proteomic","Phosphoproteomic","Polyps","Pediatric"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD061190"],"tissue":["Colon"],"sample_protocol":["Total protein from each sample was reduced, alkylated, and purified by chloroform/methanol extraction prior to digestion with MS-grade porcine trypsin/LysC (Promega). Resulting peptides were labeled using a tandem mass tag 10-plex isobaric label reagent set (Thermo) and enriched using High-Select TiO2 and Fe-NTA phosphopeptide enrichment kits in succession (Thermo) following the manufacturer’s instructions. Both enriched and un-enriched labeled peptides were separated into 46 fractions on a 100 x 1.0 mm Acquity BEH C18 column (Waters) using an UltiMate 3000 UHPLC system (Thermo) with a 40 min gradient from 99:1 to 60:40 buffer A:B ratio under basic pH conditions, and then consolidated into 18 super-fractions. Each super-fraction was then further separated by reverse phase XSelect CSH C18 2.5 um resin (Waters) on an in-line 150 x 0.075 mm column using an UltiMate 3000 RSLCnano system (Thermo). Peptides were eluted using a 75 min gradient from 98:2 to 60:40 buffer A:B ratio.Eluted peptides were ionized by electrospray (2.4 kV) followed by mass spectrometric analysis on an Orbitrap Eclipse Tribrid mass spectrometer (Thermo) using multi-notch MS3 parameters. MS data were acquired using the FTMS analyzer in top-speed profile mode at a resolution of 120,000 over a range of 375 to 1500 m/z. Following CID activation with normalized collision energy of 31.0, MS/MS data were acquired using the ion trap analyzer in centroid mode and normal mass range. Using synchronous precursor selection, up to 10 MS/MS precursors were selected for HCD activation with normalized collision energy of 55.0, followed by acquisition of MS3 reporter ion data using the FTMS analyzer in profile mode at a resolution of 50,000 over a range of 100-500 m/z.  Buffer A = 0.1% formic acid, 0.5% acetonitrile Buffer B = 0.1% formic acid, 99.9% acetonitrile Both buffers adjusted to pH 10 with ammonium hydroxide for offline separation"],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Proteins were identified and reporter ions quantified by searching the UniprotKB database restricted to Homo sapiens (January 2023) using MaxQuant (Max Planck Institute, version 2.1.4.0) with a parent ion tolerance of 3 ppm, a fragment ion tolerance of 0.5 Da, a reporter ion tolerance of 0.001 Da, trypsin/P enzyme with 2 missed cleavages, variable modifications including oxidation on M, Acetyl on Protein N-term, and phosphorylation on STY, and fixed modification of Carbamidomethyl on C.  Protein identifications were accepted if they could be established with less than 1.0% false discovery.  Proteins identified only by modified peptides were removed. Protein probabilities were assigned by the Protein Prophet algorithm [Anal. Chem. 75: 4646-58 (2003)]. TMT MS3 reporter ion intensity values are analyzed for changes in total protein using the unenriched lysate sample.  Phospho(STY) modifications were identified using the samples enriched for phosphorylated peptides. The enriched and un-enriched samples are multiplexed using two TMT10-plex batches, one for the enriched and one for the un-enriched samples Following data acquisition and database search, the MS3 reporter ion intensities were normalized using ProteiNorm (Graw et al). The data was normalized using VSN (Huber et al) and analyzed using proteoDA to perform statistical analysis using Linear Models for Microarray Data (limma) with empirical Bayes (eBayes) smoothing to the standard errors (Thurman et al, Ritchie et al).  A similar approach is used for differential analysis of the phosphopeptides, with the addition of a few steps. The phosphosites were filtered to retain only peptides with a localization probability > 75%, filter peptides with zero values, and log2 transformed. Limma was also used for differential analysis.  Proteins and phosphopeptides with an FDR-adjusted p-value < 0.05 and an absolute fold change > 2 were considered significant."],"omics_type":["Proteomics"],"labhead":["Michael P. Washburn"],"instrument_platform":[""],"submission_type":["COMPLETE"],"labhead_affiliation":["Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS USA"],"species":["Homo Sapiens (human)"],"submitter_mail":["dprovince@uams.edu"],"publication":["41969555 Attard TM, St Peter SD, Kats A, Lagemann DR, Lawson CE, Roy BC, Yusuf K, Harvey L, Bhanja P, Chugh RM, Saha S, Washburn MP, Umar S. Molecular and regional characterization of colorectal polyps: insights from proteomics, phosphoproteomics, and immune profiling. Transl Gastroenterol Hepatol. 2026 11:44 10.21037/tgh-2025-138"],"submitter_affiliation":["UAMS"],"submitter_country":["United States"],"doi":["10.6019/PXD061190"],"pubmed_abstract":["<h4>Background</h4>Familial adenomatous polyposis (FAP) is an inherited predisposition to colorectal cancer and characterized by profuse colorectal adenomas starting from the second decade of life. Regional (left <i>vs.</i> right) differences in the colonic microbiologic and immunologic microenvironment may impact adenoma evolution but are poorly understood. We aimed to characterize regional molecular, microbial, DNA damage, and immune differences in pediatric FAP polyps to test the hypothesis that polyps in pediatric FAP exhibit distinct regional and molecular features that contribute to differential growth and genomic instability.<h4>Methods</h4>Colonic polyps and adjacent non-polyp mucosa were harvested from pediatric FAP patients undergoing colonoscopy. Tandem mass tag-based proteomic and phosphoproteomic profiling was performed and were followed by functional assays including colony formation, spheroid growth, and patient-derived organoid culture. γH2AX staining was used to quantify induction of DNA double-strand breaks (DSBs) in HCT116 colon cancer cells cultured in <i>Fusobacterium nucleatum</i> conditioned media (<i>Fn</i>CM). Immunohistochemistry and immunofluorescence were used to assess ATR, CDK4, γH2AX, and oxidative damage (8-OxoG). Immune profiling was performed by flow cytometry, focusing on CD103<sup>+</sup> tissue-resident memory T cells (TRMs).<h4>Results</h4>Right-sided polyps exhibited increased ATR and CDK4 expression compared with left-sided lesions and adjacent mucosa. <i>Fn</i>CM exposure induced a marked increase in γH2AX staining in HCT116 cells, consistent with our <i>in vivo</i> findings of elevated DSB burden in proximal versus distal FAP polyps. Biofilm enrichment and higher microbial staining were observed in right-sided lesions, whereas distal polyps were enriched with CD103<sup>+</sup> TRM populations. Pharmacologic inhibition of ATR or CDK4 significantly suppressed both colony formation and spheroid growth. Organoids derived from proximal colon polyps exhibited accelerated growth and crypt budding, with higher expression of stemness markers (CD44, CD133, Lgr5, BMI-1) compared with distal polyps.<h4>Conclusions</h4>Integrated proteomic, phosphoproteomic, and immune-microbiome profiling reveals regional heterogeneity of adenomas in pediatric FAP. Right compared to left sided polyps harbor greater DNA damage, elevated ATR/CDK4 kinase activity, reduced immune surveillance, and increased stem-like growth. These findings identify ATR and CDK4 as potential therapeutic targets and suggest that regional microenvironmental differences can impact chemoprevention strategies in pediatric FAP."],"pubmed_title":["Molecular and regional characterization of colorectal polyps: insights from proteomics, phosphoproteomics, and immune profiling."],"pubmed_authors":["Attard Thomas M TM, St Peter Shawn D SD, Kats Alexander A, Lagemann Doug R DR, Lawson Caitlin E CE, Roy Badal C BC, Yusuf Kafayat K, Harvey Lisa L, Bhanja Payel P, Chugh Rishi Man RM, Saha Subhrajit S, Washburn Michael P MP, Umar Shahid S"],"additional_accession":[]},"is_claimable":false,"name":"Proteomic and Phosphoproteomic Analysis of Pediatric Familial Adenomatous Polyposis","description":"Polyps and non-polyp mucosal specimens were harvested from pediatric Familial Adenomatous Polyposis patients.  The proteome and phosphoproteome of each sample was then analyzed using the tandem mass tag system on an Orbitrap Eclipse Tribrid mass spectrometer followed by data analysis with MaxQuant, ProteiNorm, proteoDA, and ProteoViz.","dates":{"publication":"2026-04-27","submission":"2025-02-25"},"accession":"PXD061190","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:309807","NEWT:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:263737","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:4442","NEWT:192875","NEWT:1214915","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:5759","NEWT:1736231","NEWT:5518","NEWT:1392","NEWT:498217","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:935293","NEWT:375146","NEWT:118698","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:9483","NEWT:333760","NEWT:1513458","NCBITaxon:40559","NEWT:506599","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:983964","NEWT:118499","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:8694","NEWT:4093","NEWT:4096","NEWT:8692","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:1226408","NEWT:7108","NEWT:40479","NEWT:4076","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:4084","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8655","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:407821","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:28532","NEWT:353152","NEWT:8496","NEWT:27448","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:1080772","NEWT:519","NEWT:8479","NEWT:8485","NEWT:6063","NEWT:49240","NEWT:104395","NEWT:6289","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:469008","NEWT:256318","NEWT:9321","NEWT:206411","NCBITaxon:6191","NEWT:596153","NEWT:229533","NEWT:1836","NEWT:80863","NEWT:105231","NEWT:52638","NEWT:57075","NEWT:4097","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:9785","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NCBITaxon:780","NCBITaxon:1502","NEWT:6282","NEWT:1134506","NEWT:38783","NEWT:4006","NEWT:6426","NCBITaxon:5476","NEWT:6669","NEWT:9935","NEWT:89453","NEWT:287889","NEWT:51515","NEWT:588596","NEWT:51511","NEWT:8845","NEWT:92867","NEWT:92866","NEWT:5334","NEWT:51750","NEWT:202950","NEWT:382352","NEWT:413071","NCBITaxon:714","NEWT:632957","NEWT:9925","NEWT:89462","NCBITaxon:9606","NEWT:8839",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