Proteomics analysis of mouse adipose-derived mesenchymal stem cells (MSCs)
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): Stem Cell, Adipose Tissue
SUBMITTER: 
Jeonghun Yeom
LAB HEAD: Jee-Heon Jeong
PROVIDER: PXD059377 | Pride | 2026-04-17
REPOSITORIES: Pride
Dataset's files
Items per page: 5 1 - 5 of 19 |
Similar Datasets
Project description:For proteomic analysis, ADSCs from four independent donors were analyzed (n = 4 biological replicates per condition, OM vs. SM). Cell pellets were lysed in 5% sodium de-oxycholate buffer containing TCEP and CAA, supplemented with protease and phospha-tase inhibitors, followed by sonication and incubation at 60 °C. Protein concentration was determined by BCA assay, and 25 µg of protein was processed with a modified FASP pro-tocol employing 30 kDa filters. After trypsin/LysC digestion, peptides were purified on Waters HLB plates, eluted with 70% acetonitrile/0.1% TFA, dried, and stored at −80 °C. Background: Adipose-derived mesenchymal stem/stromal cells (ADSCs) are gaining recognition in regenerative medicine thanks to their potential for adipogenic, osteogenic, and chondrogenic differentiation, as well as their immunomodulatory properties. How-ever, ADSC-based therapies focus either on differentiation for tissue replacements or on counteracting the unrestrained inflammation to prevent tissue destruction and initiate re-generation. Here, we aim to examine the immunomodulatory potential of osteogenically differentiated ADSCs by analyzing their proteomic profile. Methods: using the LC-MS/MS technique, we created the proteomic profile of differentiated and undifferentiated ADSCs, and compared them with the Reactome database. The transcriptomic analysis was also performed and compared to the proteomic profile. Results: the comparison of proteomic (499 up-regulated; 355 down-regulated) and transcriptomic (212 up-regulated; 232 down-regulated) profiles showed 60,1% concordance – both proteins and transcripts showed the same trend. Significantly upregulated proteins in differentiating ADSCs (−log₁₀ p >5 and >10) were grouped into four categories: propensity for osteogenic differen-tiation; immunomodulation/immune/inflammatory response; cell senescence; cell cycle regulation. Among those proteins, thirteen were reported to play some role in processes such as immunomodulation, inflammatory signaling, transplant rejection, or graft-versus-host disease. Conclusions: we observed that differentiating ADSCs might still exert immunomodulatory effects, which could be used in the treatment of e.g., GvHD.
2026-04-27 | PXD073297 | Pride
Project description:Label-free protein sequencing is critically enabled by bottom-up, mass spectrometry-based proteomics workflows. Applications such as antibody sequencing or antigen discovery require de novo reconstruction of peptide and protein sequences. While trypsin has long served as the gold-standard protease in proteomics, its restricted C-terminal cleavage specificity constrains peptide diversity, particularly limiting coverage in antibody hypervariable complementarity-determining regions (CDRs). As a result, current workflows yield sparse reads and sequence gaps. Although multi-protease and hybrid-fragmentation strategies can notably improve coverage, they add complexity and compromise scalability and reproducibility. Here, we present a novel approach using HyperThermoacidic Archaeal (HTA) proteases Krakatoa or Vesuvius as powerful single-enzyme solutions for de novo antibody sequencing. Each protease generated over five times more unique peptide reads than trypsin or chymotrypsin with high redundancy across CDRs. Combined with EAciD fragmentation on a ZenoTOF 7600 system, this workflow enabled complete, unambiguous antibody sequencing. Despite most de novo tools being optimized for CID/HCD-tryptic data, analysis using PEAKS/DeepNovo and Stitch softwares showed that HTA-Proteases yielded up to fourfold higher alignment scores and fewer sequence mistakes across variable regions. Redundant reads increased more than threefold compared to standard proteases, boosting confidence in amino acid assignment and reducing ambiguity in final assemblies. Our alternative HTA-EAciD approach offers short digestion times, eliminates extensive cleanup, and enables analysis in a single LC-MS/MS run. This single-protease strategy delivers sequencing performance comparable to multi-enzyme workflows, providing a scalable, efficient, and highly confident approach for de novo sequencing in antibody discovery and beyond.
2026-03-17 | PXD063988 | Pride
Project description:Background. Leptospirosis is among the most widespread zoonoses worldwide. Severe pulmonary hemorrhagic syndrome (SPHS) represents a serious complication of leptospirosis, with poor understanding of its underlying mechanisms and an urgent need for identification of effective biomarkers. Methods. A nested case-control analysis of the blood specimens obtained from two previous multi-center cohorts was conducted. Candidate microRNAs were initially discovered through a global profiling of 800 serum microRNAs, then validated using real-time polymerase-chain reactions. We further conducted a multi-omics analysis incorporating transcriptomic and proteomic data to identify enriched pathways through which the newly identified microRNAs could regulate. Findings. A total of 28 SPHS and 140 non-SPHS patients were evaluated by serum microRNA profiling, revealing distinct expression patterns between the two phenotypes. From the top 81 significantly expressed microRNAs, seven were selected for validation. Among these, miR-5010-3p and miR-147b-3p had area under the curve (AUC) values of 0.72 (95% CI: 0·62–0·81) and 0·66 (95% CI: 0·55–0·76) for discriminating SPHS. Notably, the two microRNAs could detect SPHS in patients who were yet to manifest chest radiograph shadows at the time of sample collection, and in a subgroup of patients who were recruited on day 2 of illness or earlier, with consistent AUC values. Integrated gene-protein pathway enrichment analysis revealed numerous pathways involving host immune responses. Among these, the tumor necrosis factor signaling pathway was the most significant with many of its member genes being targeted by miR-5010-3p or miR-147b-3p.
2026-02-09 | PXD052319 | Pride
Project description:Loiasis, caused by the filarial nematode Loa loa, imposes a significant burden of disease in endemic regions in West and Central Africa. Manifestations include microfilaria in the blood (MF) and migration of the adult eye worm (EW), with clinical presentations ranging from asymptomatic infections to life threatening organ involvement. The diagnostic gold standard, microscopic detection of microfilaria in the blood, remains difficult due to widely varying microfilaria counts, frequent amicrofilaraemia in patients with EW, and unreliable serological assays. By applying high-throughput plasma proteomics, we investigated the human host response in 274 patients with different L. loa disease states (INF), including EW (n=148), MF (n=42), or both (EWMF; n=84), compared to 136 loa-negative (LN) controls. Five proteins were elevated in INF compared to LN, including IGHG3, IGHG4, and LCP1. Four followed the trend from LN to EW to MF and EWMF, reflecting a more pronounced host response to higher microfilaria couMoMoreover, IGHG4 correlated positively with eosinophil and microfilarial counts underlining its role in chronic, parasitic infections. 63 plasma proteins exhibited notable differences depending on self-reported symptoms. The proteomic signature allowed for accurate classification of EW (AUROC = 0.73) and microfilaria positive (0.84) individuals. Together, L. loa infection leads to relevant alterations of the host plasma proteome, highlighting the importance of further in-depth research on this highly neglected parasitic disease. Here, we present additional experiments to validate IGHG4, IGHG3, LCP1, ACTBL2 and IGLV9-49 as proteomic biomarkers for Loa Loa Infection.
2025-07-14 | PXD063487 | Pride
Project description:Untargeted DIA/SWATH of the whole cell proteome of Mycobacterium tuberculosis CRISPRi mutants
2023-12-21 | PXD041697 | Pride
Project description:Pancreatic ductal adenocarcinoma (PDAC), with its devastating prognosis and limited treatment options, necessitates innovative therapeutic strategies. T-cell-based immunotherapy has shown promise for various cancers, including PDAC. Thus, a comprehensive understanding of the HLA-peptidome in PDAC is essential to pave the way for the effective design of immunotherapy and other interventions. In this study, we employed off-line high-pH reverse-phase (HPH-RP) fractionation of peptides extracted from immunoaffinity purified HLA class I molecules isolated from the surface of Panc1 cells in the absence and presence of cytokine stimulation. We demonstrate that this strategy is a relatively simple and rapid technique that significantly expands the depth of coverage of the PDAC immunopeptidome using data-dependent acquisition strategies and allowing the identification of more potentially actionable peptide antigens. Whilst cell lines provide an abundant source of material for immunopeptidomics analysis, clinical samples and biopsies from pancreatic cancer patients typically involve much smaller amounts of material. Thus, we performed a proof of concept study and demonstrated that immunopeptidome characterization was feasible from cell pellets of only 1 million cells (equivalent to approximately 1mg of tissue), using a spectral library generated from the HPH-RP fractionated material and the ZenoSWATH DIA-MS workflow on the SCIEX 7600 ZenoToF system. These studies form the basis for future clinical translational immunopeptidomics approaches to screen tumor antigen presentation in PDAC biopsies and provide new opportunities for immune-based therapies.
2025-07-14 | PXD054360 | Pride
Project description:Pancreatic ductal adenocarcinoma (PDAC), with its devastating prognosis and limited treatment options, necessitates innovative therapeutic strategies. T-cell-based immunotherapy has shown promise for various cancers, including PDAC. Thus, a comprehensive understanding of the HLA-peptidome in PDAC is essential to pave the way for the effective design of immunotherapy and other interventions. In this study, we employed off-line high-pH reverse-phase (HPH-RP) fractionation of peptides extracted from immunoaffinity purified HLA class I molecules isolated from the surface of Panc1 cells in the absence and presence of cytokine stimulation. We demonstrate that this strategy is a relatively simple and rapid technique that significantly expands the depth of coverage of the PDAC immunopeptidome using data-dependent acquisition strategies and allowing the identification of more potentially actionable peptide antigens. Whilst cell lines provide an abundant source of material for immunopeptidomics analysis, clinical samples and biopsies from pancreatic cancer patients typically involve much smaller amounts of material. Thus, we performed a proof of concept study and demonstrated that immunopeptidome characterization was feasible from cell pellets of only 1 million cells (equivalent to approximately 1mg of tissue), using a spectral library generated from the HPH-RP fractionated material and the ZenoSWATH DIA-MS workflow on the SCIEX 7600 ZenoToF system. These studies form the basis for future clinical translational immunopeptidomics approaches to screen tumor antigen presentation in PDAC biopsies and provide new opportunities for immune-based therapies.
2025-07-14 | PXD054417 | Pride
Project description:Globally, over 65 million individuals are estimated to suffer from post-acute sequelae of COVID-19 (PASC). A large number of individuals living with PASC experience cardiovascular symptoms (i.e. chest pain and heart palpitations) (PASC-CVS). The role of chronic inflammation in these symptoms, in particular in individuals with symptoms persisting for >1 year after SARS-CoV-2 infection, remains to be determined. Here, we show that compared to individuals with a resolved SARS-CoV-2 infection (and no persistent symptoms), individuals with prolonged PASC-CVS had elevated levels of pro-inflammatory cytokines. However, these cytokines were found to be present in trace amounts, such that they could only be detected with the use of novel nanotechnology. Importantly, these trace-level cytokines had a direct effect on the functionality of primary human cardiomyocytes in vitro. Proteomics analyses demonstrated further differences in PASC-CVS and recovered plasma including increased abundance of complement and coagulation associated proteins.
2024-11-01 | PXD050202 | Pride
Project description:This study explored the molecular mechanisms underlying oat grain development in two oat varieties, Bannister and Bilby, with a focus on lipid biosynthesis.
2025-04-04 | PXD058633 | Pride
Project description:A novel henipavirus (HNV) named Langya virus (LayV) was isolated in human patients in China in August 2022. It is closely related to Mòjiāng virus (MojV) and represents the first instance of HNV zoonosis to humans outside of Nipah virus (NiV) and Hendra viruses (HeV). Within this work, mass spectrometry glycoproteomic analysis revealed that although the LayV F protein has reduced glycosylation compared to its NiV and HeV counterparts, a unique glycan was identified positioned at the DIII apex, shielding a previously identified site of vulnerability in NiV F.
2023-05-03 | PXD039898 | Pride