{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Msf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_alone_vs_Co-culture1.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_alone_vs_Co-culture1.msfView"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_alone_SET2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_CoCulture_SET3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_CoCulture_SET1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_alone_SET1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_alone_SET3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_CoCulture_SET2.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_alone_vs_Co-culture.pdResultView","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Dr.Mohini_Proteomics_Data_Analysis_25April_26.pdStudy","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Dr.Mohini_Proteomics_Data_Analysis_25April_26.pdStudy.bak","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077957/Apo_WJ_alone_vs_Co-culture.pdResult"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["draranjitmd@gmail.com"],"submitter":["Ranjit Sahoo"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"disease":["Graft-versus-host Disease"],"software":[""],"submitter_keywords":["Metabolic shift","Acute graft-versus-host-disease","Immunomodulation","Hypoxia","Secretome","Antioxidant","Tissue repair","Apoptosis","Mesenchymal stem cells"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD077957"],"tissue":["Umbilical Cord","Stem Cell","Blood"],"sample_protocol":["Protein per sample (WJ-MSCs, WJ-MSCsHYP+APO, and their co-culture with aPBMNCs) was used for digestion and reduced with 5 mM tris(2-carboxyethyl) phosphine (TCEP) and further alkylated with 50 mM iodoacetamide and then digested with Trypsin (1:50, Trypsin/lysate ratio) for 16 h at 37 °C. Digests were cleaned using a C18 silica cartridge to remove the salt and dried using a speed vac. The dried pellet was resuspended in buffer A (2% acetonitrile, 0.1% formic acid)."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Experiments were performed on an Easy-nlc-1000 system coupled with an Orbitrap Exploris mass spectrometer. 1µg of peptide sample was loaded on C18 column 15 cm, 3.0μm Acclaim PepMap (Thermo Fisher Scientific, USA) and separated with a 0–40% gradient of buffer B (80% acetonitrile, 0.1% formic acid) at a flow rate of 500 nl/min) and injected for MS analysis. LC gradients were run for 110 minutes. MS1 spectra were acquired in the Orbitrap (Max IT = 60ms, AGQ target = 300%; RF Lens = 70%; R=60K, mass range: 375−1500; Profile data). Dynamic exclusion was employed for 30s, excluding all charge states for a given precursor. MS2 spectra were collected for the top 20 peptides. MS2 (Max IT= 60ms, R= 15K, AGC target 100%). All samples were processed, and the RAW files generated were analyzed with Proteome Discoverer (v2.5) against the UniProt Human database. For dual Sequest and Amanda search, the precursor and fragment mass tolerances were set at 10 ppm and 0.02 Da, respectively. The protease used to generate peptides, i.e., enzyme specificity, was set for trypsin/P (cleavage at the C terminus of “K/R: unless followed by “P”). Carbamidomethyl on cysteine as fixed modification and oxidation of methionine and N-terminal acetylation were considered as variable modifications for database search.  Both peptide spectrum match and protein false discovery rate were set to 0.01 FDR."],"omics_type":["Proteomics"],"labhead":["Prof. Ranjit Kumar Sahoo"],"instrument_platform":[""],"labhead_affiliation":["All India Institute of Medical Sciences, New Delhi, India"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["drranjitmd@gmail.com"],"publication":["Not available"],"submitter_affiliation":["All India Institute of Medical Sciences, New Delhi"],"submitter_country":["India"],"additional_accession":[]},"is_claimable":false,"name":"Dual Preconditioned Mesenchymal Stem Cells-Derived Secretome Augment Immunomodulation and Drive Metabolic Reprogramming in Acute Graft-versus-Host Disease","description":"The immune plasticity of the host critically influences disease progression and therapeutic outcomes. In acute graft-versus-host disease (aGVHD), conventional conditioning regimens often induce toxicity, underscoring the need for effective adjunctive strategies to restore immune balance. This study evaluates the immunomodulatory and regenerative potential of secretome derived from naive and preconditioned human mesenchymal stem cells (MSCs) in aGVHD. Human MSCs from bone marrow and Wharton’s Jelly were preconditioned under hypoxia (1% O₂), apoptosis (1 µM staurosporine, 24 h), or both (dual preconditioning), and their secretome was assessed for immunoregulatory and antioxidant effects using T-cell proliferation assays, Treg induction, and M1-to-M2 macrophage polarization. Cellular bioenergetics and mitochondrial function were analyzed to explore metabolic reprogramming. Mechanistic insights were obtained through LC-MS/MS-based proteomic profiling of CCM co-cultured with aGVHD patient-derived activated PBMNCs, and in vivo efficacy was validated in a chemotherapy-induced aGVHD murine model. Dual preconditioned WJ-MSCs (WJ-MSCsHYP+APO)-derived secretome exhibited superior immunomodulatory activity, suppressing T-cell proliferation, enhancing Treg and Th2/Th9 differentiation, and promoting M2 macrophage polarization. It reduced mitochondrial ROS, improved mitochondrial polarization, and shifted T-cell metabolism from glycolysis to oxidative phosphorylation. Proteomic analysis revealed downregulation of IL-12, IL-17, and JAK–STAT signaling, along with modulation of complement, coagulation, and metabolic pathways. Secretome also enhanced extracellular matrix remodeling and antioxidant responses, supporting tissue repair. Dual preconditioning significantly amplifies the immunoregulatory, antioxidant, and regenerative efficacy of WJ-MSCs-derived secretome, presenting a promising non-cellular therapeutic approach for aGVHD management.","dates":{"publication":"2026-05-04","submission":"2026-05-03"},"accession":"PXD077957","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:1211601","NEWT:876138","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:10029","NEWT:1000589","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:499175","NEWT:476272","NEWT:3747","NEWT:367830","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:28038","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:4081","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:2829","NEWT:216599","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:260707","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NCBITaxon:6073","NEWT:884204","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:38783","NEWT:8727","NEWT:4006","NEWT:8726","NEWT:6426","NEWT:6669","NEWT:10090","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:5334","NEWT:37334","NEWT:382352","NCBITaxon:10359","NEWT:242619","NEWT:632957","NEWT:373995","NEWT:5689","NEWT:544404","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:2758385","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:714","NEWT:421932","NEWT:196627","NEWT:5691","NEWT:48479","NEWT:627025","NEWT:1097677","NEWT:61674","NEWT:1117957","NEWT:9913","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:180066","NEWT:135588","NEWT:1843183","NEWT: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