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Hekkala"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"disease":["Obesity","Type 2 Diabetes Mellitus"],"software":["Not available"],"submitter_keywords":["Gut microbiota","Obesity","Extracellular vesicles"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD050033"],"sample_protocol":["EVs were isolated from fecal samples by protocol earlied desceribed by Byts et al 2023. EV protein isolation was performed using methanol chloroform precipitation according to Friedman 200724. Shortly, 1 volume vesicles added with 3 volume water, 4 volume methanol and 1 volume chloroform. Appeared precipitate was washed adding again 4 volume methanol and centrifuged precipitate to bottom of the tube. The precipitate was dried and dissolved to 1x Laemly loading buffer (Bio-Rad, USA) and water by boiling 5 min. The samples were loaded to 12% Mini-Protean TGX (Bio-Rad) gel and SDS-PAGE electrophoresis were performed at 110 V until samples were completely in the gel, roughly 10 minutes. The gel was fixed in 50% ethanol and 10 % acetic acid solution for 30 min and rinsed with water. The gel was stained by SYPRO Ruby protein gel stain (Thermo Fisher Scientific) at overnight. Excess dye was removed by washing with 5 % acetic acid for 5 min and in dd water 15 min. Gel was dried by ethanol for transport. Before mass spectrometry, samples were in-gel digested via trypsin and peptides were dissolved in 0.1 % formic acid. The LC-ESI-MS/MS analyses were performed on a nanoflow HPLC system (Easy-nLC1200, Thermo Fisher Scientific) coupled to the Q Exactive HF mass spectrometer (Thermo Fisher Scientific) equipped with a nano-electrospray ionization source. Mass spectrometry analysis was performed at the Turku Proteomics Facility, University of Turku and Åbo Akademi University."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Sequences of proteomic samples were analyzed by PEAKS Studio software (version 10.6) (bioinformatics Solutions Inc., USA). For protein and peptide identification the database search was performed against Uniprot Swissprot and Uniprot trEMBL databases (v.2022_05) with parent mass error tolerance 10.0 ppm, fragment mass error tolerance 0.02 Da and FDR for both was 1.0%. Only top protein from each protein group were accepted. Proteins were identified to present if at least one unique peptide with total coverage of supporting peptide was more than 1%. Proteins presenting in negative control sample and blank were excluded from identification results."],"omics_type":["Proteomics"],"labhead":["Justus Reunanen"],"instrument_platform":[""],"labhead_affiliation":["Department of translational medicine, medical faculty, university of Oulu, Finland"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["38191968 Zhao S, Hörkkö S, Savolainen MJ, Koivukangas V, Mäkinen VP, Ala-Korpela M, Hukkanen J. Short-Term Metabolic Changes and Their Physiological Mediators in the Roux-en-Y Gastric Bypass Bariatric Surgery. Obes Surg. 2024 34(2):625-634 10.1007/s11695-023-07042-y","10.1111/MMI.70064","33246847 Härma MA, Adeshara K, Istomin N, Lehto M, Blaut M, Savolainen MJ, Hörkkö S, Groop PH, Koivukangas V, Hukkanen J. Gastrointestinal manifestations after Roux-en-Y gastric bypass surgery in individuals with and without type 2 diabetes. Surg Obes Relat Dis. 2021 17(3):585-594 10.1016/j.soard.2020.10.021"],"submitter_mail":["jenni.hekkala@oulu.fi"],"submitter_affiliation":["Department of translational medicine, Medical faculty,University of Oulu"],"submitter_country":["Finland"],"pubmed_abstract":["

Background

The Roux-en-Y gastric bypass (RYGB) is a common bariatric surgery to treat obesity. Its metabolic consequences are favourable and long-term clinical corollaries beneficial. However, detailed assessments of various affected metabolic pathways and their mediating physiological factors are scarce.

Methods

We performed a clinical study with 30 RYGB patients in preoperative and 6-month postoperative visits. NMR metabolomics was applied to profiling of systemic metabolism via 80 molecular traits, representing core cardiometabolic pathways. Glucose, glycated haemoglobin (HbA1c), insulin, and apolipoprotein B-48 were measured with standard assays. Logistic regression models of the surgery effect were used for each metabolic measure and assessed individually for multiple mediating physiological factors.

Results

Changes in insulin concentrations reflected those of BMI with robust decreases due to the surgery. Six months after the surgery, triglycerides, remnant cholesterol, and apolipoprotein B-100 were decreased -24%, -18%, and -14%, respectively. Lactate and glycoprotein acetyls, a systemic inflammation biomarker, decreased -16% and -9%, respectively. The concentrations of branched-chain (BCAA; leucine, isoleucine, and valine) and aromatic (phenylalanine and tyrosine) amino acids decreased after the surgery between -17% for tyrosine and -23% for leucine. Except for the most prominent metabolic changes observed for the BCAAs, all changes were almost completely mediated by weight change and insulin. Glucose and type 2 diabetes had clearly weaker effects on the metabolic changes.

Conclusions

The comprehensive metabolic analyses indicate that weight loss and improved insulin sensitivity during the 6 months after the RYGB surgery are the key physiological outcomes mediating the short-term advantageous metabolic effects of RYGB. The clinical study was registered at ClinicalTrials.gov as NCT01330251.","

Background

Roux-en-Y gastric bypass (RYGB) surgery is an effective treatment for obesity, which improves cardiovascular health and reduces the risk of premature mortality. However, some reports have suggested that RYGB may predispose patients to adverse health outcomes, such as inflammatory bowel disease (IBD) and colorectal cancer.

Objectives

The present prospective study aimed to evaluate the impact of RYGB surgery on cardiovascular risk factors and gastrointestinal inflammation in individuals with and without type 2 diabetes (T2D).

Setting

University hospital setting in Finland.

Methods

Blood and fecal samples were collected at baseline and 6 months after surgery from 30 individuals, of which 16 had T2D and 14 were nondiabetics. There were also single study visits for 6 healthy reference patients. Changes in cardiovascular risk factors, serum cholesterol, and triglycerides were investigated before and after surgery. Fecal samples were analyzed for calprotectin, anti-Saccharomyces cerevisiae immunoglobulin A antibodies (ASCA), active lipopolysaccharide (LPS) concentration, short-chain fatty acids (SCFAs), intestinal alkaline phosphatase activity, and methylglyoxal-hydro-imidazolone (MG-H1) protein adducts formation.

Results

After RYGB, weight decreased on average -21.6% (-27.2 ± 7.8 kg), excess weight loss averaged 51%, and there were improvements in cardiovascular risk factors. Fecal calprotectin levels (P < .001), active LPS concentration (P < .002), ASCA (P < .02), and MG-H1 (P < .02) values increased significantly, whereas fecal SCFAs, especially acetate (P < .002) and butyrate (P < .03) levels, were significantly lowered.

Conclusion

The intestinal homeostasis is altered after RYGB, with several fecal markers suggesting increased inflammation; however, clinical significance of the detected changes is currently uncertain. As chronic inflammation may predispose patients to adverse health effects, our findings may have relevance for the suggested association between RYGB and increased risks of incident IBD and colorectal cancer."],"pubmed_title":["Gastrointestinal manifestations after Roux-en-Y gastric bypass surgery in individuals with and without type 2 diabetes.","Short-Term Metabolic Changes and Their Physiological Mediators in the Roux-en-Y Gastric Bypass Bariatric Surgery."],"pubmed_authors":["Härma Mari-Anne MA, Adeshara Krishna K, Istomin Natalie N, Lehto Markku M, Blaut Michael M, Savolainen Markku J MJ, Hörkkö Sohvi S, Groop Per-Henrik PH, Koivukangas Vesa V, Hukkanen Janne J","Zhao Siyu S, Hörkkö Sohvi S, Savolainen Markku J MJ, Koivukangas Vesa V, Mäkinen Ville-Petteri VP, Ala-Korpela Mika M, Hukkanen Janne J"],"additional_accession":[]},"is_claimable":false,"name":"Gut microbiota -derived extracellular vesicles in patients with obesity undergoing gastric bypass surgery","description":"30 obese patients undergo gastric bypass. Fecal samples were collected at baseline and 6 months after the surgery and also 9 healty subjects. EVs were isolated from feces and proteins were isolated from purified EV prep.","dates":{"publication":"2026-04-25","submission":"2024-02-22"},"accession":"PXD050033","cross_references":{"TAXONOMY":["NEWT:108018","NEWT:377960","NEWT:1131","NEWT:2042546","NEWT:295546","NEWT:258594","NEWT:1126","NEWT:1129","NEWT:309807","NEWT:89184","NEWT:309800","NEWT:1323429","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:10034","NEWT:661410","NEWT:224326","NEWT:376619","NEWT:3765","NEWT:3767","NEWT:135622","NEWT:672127","NEWT:656061","NEWT:37965","NEWT:656064","NEWT:3760","NEWT:36630","NEWT:381198","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:44250","NEWT:317447","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:12637","NEWT:2164133","NEWT:2767846","NEWT:314344","NEWT:108061","NEWT:224308","NEWT:49928","NEWT:160621","NEWT:110368","NEWT:1916073","NEWT:1310161","NEWT:1230383","NEWT:77133","NEWT:1310165","NEWT:5516","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:1310173","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:419481","NEWT:5507","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:709964","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:3715","NEWT:2065263","NEWT:1549675","NEWT:177437","NEWT:9014","NEWT:10891","NEWT:1616117","NEWT:34865","NEWT:28174","NEWT:284812","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:1246791","NEWT:9005","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:1883426","NEWT:10886","NEWT:3708","NEWT:536231","NEWT:219813","NEWT:215451","NEWT:460519","NEWT:272844","NEWT:1348799","NEWT:55784","NEWT:485","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:216778","NEWT:376686","NEWT:237610","EFO:0001352","NEWT:219809","NEWT:219808","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:141469","NEWT:987059","NEWT:491","NEWT:460523","NEWT:85694","NEWT:85692","NEWT:3750","NEWT:291146","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:278161","NEWT:415978","NEWT:410289","NEWT:191701","NEWT:9054","NEWT:472","NEWT:29459","NEWT:1380096","NEWT:28128","NEWT:470","NEWT:41122","NEWT:1328300","NEWT:748693","NCBITaxon:50557","NEWT:29491","NEWT:911022","NEWT:446","NEWT:153481","NEWT:445","NEWT:63366","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:3726","NEWT:30455","NEWT:28141","NEWT:9031","NEWT:3728","NEWT:108931","NEWT:219799","NEWT:219798","NEWT:548","NEWT:150475","NEWT:256737","NEWT:51350","NEWT:8694","NEWT:8692","NEWT:542","NEWT:394503","NEWT:13076","NEWT:219785","NEWT:8673","NEWT:550","NEWT:10804","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:9995","NEWT:28112","NEWT:49012","NEWT:28110","NEWT:10832","NEWT:507601","NEWT:520","NEWT:64657","NEWT:186441","NEWT:643680","NEWT:214092","NEWT:40697","NEWT:13095","NEWT:162425","NEWT:242124","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:80833","NEWT:479096","NEWT:28108","NEWT:28104","NEWT:1114957","NEWT:568703","NEWT:568708","NEWT:52641","NEWT:353152","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:27689","NEWT:207769","NEWT:40674","NEWT:51329","NCBITaxon:1763","NEWT:443906","NEWT:13037","NEWT:519","NEWT:7394","NEWT:6063","NEWT:404330","NEWT:1328388","NEWT:300641","NEWT:39655","NEWT:38323","NEWT:206411","NEWT:214053","NEWT:80863","NEWT:665890","NEWT:52639","NEWT:52638","NEWT:8697","NEWT:861109","NEWT:8695","NEWT:1196866","NEWT:1045775","NEWT:1123869","NCBITaxon:1335626","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:27697","NEWT:86185","NEWT:9935","NEWT:287889","NEWT:1028307","NEWT:52603","NEWT:92867","NEWT:92866","NEWT:1344414","NEWT:202950","NEWT:741158","NEWT:1293091","NEWT:202956","NEWT:315750","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:1436183","NEWT:4232","NEWT:9922","NEWT:416348","NEWT:11298","NEWT:4236","NEWT:398031","NEWT:196627","NEWT:523840","NEWT:1076878","NEWT:200308","NEWT:200302","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:2666255","NEWT:999810","NEWT:28995","NEWT:1392998","NEWT:1150621","NEWT:1085791","NEWT:745531","NEWT:226900","NEWT:231490","NEWT:590651","NEWT:449239","NEWT:244704","NEWT:9909","NEWT:9902","NEWT:430615","NEWT:563041","NEWT:36599","NEWT:41949","NEWT:326423","NEWT:326424","NEWT:13013","NEWT:749906","NEWT:418985","NEWT:749907","NEWT:431947","NEWT:142809","NEWT:1095183","NEWT:302409","NEWT:130821","NEWT:2320211","NEWT:27606","NEWT:290610","NEWT:1519788","NEWT:59202","NEWT:9975","NEWT:8643","NEWT:1801631","NEWT:1159899","NEWT:502780","NEWT:860688","NEWT:35231","NEWT:1774208","NEWT:8644","NEWT:1125630","NEWT:28930","NEWT:202914","NEWT:27602","NEWT:502779","NEWT:297246","NEWT:483139","NEWT:101491","NEWT:8639","NEWT:8637","NEWT:1114970","NEWT:285272","NEWT:192222","NEWT:9963","NEWT:197911","NEWT:197912","NEWT:239386","NEWT:2785785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