HeLa Pro-IL-1a TurboID LC-MS/MS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Hela Cell
SUBMITTER: 
Rose Wellens
LAB HEAD: David Brough
PROVIDER: PXD053438 | Pride | 2024-06-28
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| IL1a_N1.raw | Raw | |||
| IL1a_N2.raw | Raw | |||
| IL1a_N3.raw | Raw | |||
| IL1a_N4.raw | Raw | |||
| TID_N1.raw | Raw |
Items per page: 5 1 - 5 of 12 |
Publications
Proximity labelling of pro-interleukin-1α reveals evolutionary conserved nuclear interactions.
Wellens Rose R Tapia Victor S VS Seoane Paula I PI Bennett Hayley H Adamson Antony A Coutts Graham G Rivers-Auty Jack J Lowe Martin M Green Jack P JP Lopez-Castejon Gloria G Brough David D Hoyle Christopher C
Nature communications 20240808 1
Interleukin-1α is a suggested dual-function cytokine that diverged from interleukin-1β in mammals potentially by acquiring additional biological roles that relate to highly conserved regions in the pro-domain of interleukin-1α, including a nuclear localisation sequence and histone acetyltransferase-binding domains. Why evolution modified pro-interleukin-1α's subcellular location and protein interactome, and how this shaped interleukin-1α's intracellular role, is unknown. Here we show that TurboI ...[more]
Similar Datasets
Project description:In this study, we perform (phospho)proteomics analysis of 45 pre-treatment HER2+ needle biopsies of early-stage invasive breast cancer to identify molecular signatures predictive of treatment response to Trastuzumab, Pertuzumab and chemotherapy. All patient biopsies included in this study were classified as HER2+ with a minimum tumour grade of two and tumour cell density of 60% or higher. After needle biopsies were taken, patients completed multiple drug treatment cycles according to the regime of the TRAIN2 study. Finally, treatment response was determined at surgery. The systemic treatment response was categorised as pathological complete response (pCR = ypT0/isypN0) (n=26), near pCR (npCR) (n=8), or No pCR (n=11).
2023-09-20 | PXD034643 | Pride
Project description:The incorporation of machine learning methods into proteomics workflows improves the identification of disease-relevant biomarkers and biological pathways. However, machine learning models, such as deep neural networks, typically suffer from lack of interpretability. Here, we present a deep learning approach to combine biological pathway analysis and biomarker identification to increase the interpretability of proteomics experiments. Our approach integrates a priori knowledge of the relationships between proteins and biological pathways and biological processes into sparse neural networks to create biologically informed neural networks. We employ these networks to differentiate between clinical subphenotypes of septic acute kidney injury and COVID-19, as well as acute respiratory distress syndrome of different aetiologies. To gain biological insight into the complex syndromes, we utilize feature attribution-methods to introspect the networks for the identification of proteins and pathways important for distinguishing between subtypes. The algorithms are implemented in a freely available open source Python-package (https://github.com/InfectionMedicineProteomics/BINN).
2023-09-05 | PXD044264 | Pride
Project description:The statistical validation of peptide and protein identifications in mass spectrometry proteomics is a critical step in the analytical workflow. This is particularly important in discovery experiments to ensure only confident identifications are accumulated for downstream analysis and biomarker consideration. However, the inherent nature of discovery proteomics experiments leads to scenarios where the search space will inflate substantially due to the increased number of potential proteins that are being queried in each sample. In these cases, issues will begin to arise when the machine learning algorithms that are trained on an experiment specific basis cannot accurately distinguish between correct and incorrect identifications and will struggle to accurately control the false discovery rate. Here, we propose an alternative validation algorithm trained on a curated external data set of 2.8 million extracted peakgroups that leverages advanced machine learning techniques to create a generalizable peakgroup scoring (GPS) method for data independent acquisition (DIA) mass spectrometry. By breaking the reliance on the experimental data at hand and instead training on a curated external dataset, GPS can confidently control the false discovery rate while increasing the number of identifications and providing more accurate quantification in different search space scenarios. To first test the performance of GPS in a standard experimental environment and to provide a benchmark against other methods, a novel spike-in data set with known varying concentrations was analyzed. When compared to existing methods GPS increased the nunmber of identifications by 5-18% and was able to provide more accurate quantification by increasing the number of ratio validated identifications by 24-74%. To evaluate GPS in a larger search space, a novel data set of 141 blood plasma samples from patients developing acute kidney injury after sepsis was searched with a human tissue spectral library (10000+ proteins). Using GPS, we were able to provide a 207-377% increase in the number of candidate differentially abundant proteins compared to the existing methods while maintaining competitive numbers of global identifications. Finally, using an optimized human tissue library and workflow we were able to identify 1205 proteins from the 141 plasma samples and increase the number of candidate differentially abundant proteins by 70.87%. With the addition of machine learning aided differential expression, we were able to identify potential new biomarkers for stratifying subphenotypes of acute kidney injury in sepsis. These findings suggest that by using a generalized model such as GPS in tandem with a massive scale spectral library it is possible to expand the boundaries of discovery experiments in DIA proteomics. GPS is open source and freely available on github at https://github.com/InfectionMedicineProteomics/gps
2023-07-20 | PXD038394 | Pride
Project description:Single cell transcriptomic analyses (scRNAseq) of hepatocytes and liver endothelial cells (L-EC) have revolutionized the understanding of the spatial architecture of liver structure and function. The spatial alignment of L-EC and hepatocytes is pivotal for liver function in health and disease given that L-EC act as instructive gatekeeper of nearby hepatocytes including the maintenance of liver metabolic zonation in a Wnt-dependent manner. Advancing liver biology beyond the ’transcript-centric’ view of scRNAseq analyses is presently restricted by the limited resolution of proteomics and genome-wide techniques to analyse post-translational modifications. Here, by combining spatial cell sorting methodology with transcriptomic and quantitative proteomic/phospho-proteomic analyses, we established the first functionally and spatially-resolved proteome landscape of the liver endothelium, yielding deep mechanistic insight into zonated vascular signalling mechanisms. Phosphorylation of receptor tyrosine kinases (RTK) was detected preferentially in the central vein area resulting in an atypical enrichment of tyrosine phosphorylation. Prototypic biological validation of the identified strong phosphorylation gradient of the vascular RTK Tie1 by blockade resulted in the rapid peri-central dysregulation of the L-EC transcriptome. Notably, the expression of Wnt9b in L-EC was discovered as Tie receptor controlled with reciprocal regulation by FoxO1 and STAT3 transcription factors. Genetic inactivation of Tie1 in L-EC or antibody blockade resulted in reduced liver regeneration following partial hepatectomy with reduced Wnt ligand and Wnt target gene expression, including Axin2, Sox9, Tbx3 and Lgr5. Taken together, the study has yielded unparalleled insight into the spatial organization of L EC signalling and discovered a vascular Tie-Wnt signalling axis as regulator of liver function. The employed spatial sorting technique followed by phospho-proteomic analysis may be employed as a universally adaptable strategy for the spatial phosphoproteomic analysis of scRNAseq data-defined relevant cellular (sub)-populations.
2021-05-21 | PXD020805 | Pride
Project description:Venous thromboembolism (VTE) comprising deep venous thrombosis and pulmonary embolism is a main cause of morbidity and mortality that causes tremendous health care costs. Short term immobility related conditions arising from hospitalization, acute trauma and forced bed rest are major risk factors for the development of VTE. In contrast, chronically paralyzed patients with post-spinal cord injury are protected from VTE despite immobilization. Similarly, free-ranging brown bears (Ursus arctos) that hibernate (immobilize) have adapted to this threat through yet to be discovered mechanisms and do not develop VTE. This suggests that long-term immobility can induce antithrombotic mechanisms that are evolutionarily conserved. Here we aimed to identify these adaptive mechanisms of VTE protection in a cross-species approach. Mass spectrometry-based proteomics identified platelet expressed heat shock protein 47 (Hsp47) as the most substantially downregulated protein during brown bear hibernation. In a clinical bed rest study and in spinal-cord injured humans, we likewise observed drastic reduction of platelet-expressed Hsp47. Genetic ablation and pharmaceutical inhibition of platelet Hsp47 attenuates deep vein thrombosis and thromboinflammatory responses in mice and human blood cells. This suggests that Hsp47 downregulation is an evolutionarily conserved mechanism that also protects immobilized patients from VTE. Our translational approach thus identified an antithrombotic signature that may give rise to novel antithrombotic therapeutics and prognostic markers.
2023-04-14 | PXD030465 | Pride
Project description:Chemical crosslinking mass spectrometry is rapidly emerging as a prominent technique to study protein structures. Structural information is obtained by covalently connecting peptides in close proximity by small reagents and identifying the resulting peptide pairs by mass spectrometry. However, sub-stoichiometric reaction efficiencies render routine detection of crosslinked peptides problematic. Here we present a new tri-functional crosslinking reagent, termed PhoX, which is decorated with a stable phosphonic acid handle. This makes the crosslinked peptides amenable to the well-established IMAC enrichment. The handle allows for 300x enrichment efficiency and 97% specificity, dramatically reducing measurement time and improving data quality. We exemplify the approach on various model proteins and protein complexes, e.g. resulting in a structural model of LRP1/RAP complex. PhoX is also applicable to whole cell lysates. When focusing the database search on ribosomal proteins, our first attempt resulted in 355 crosslinks, out-performing current efforts in less measurement time.
2019-09-13 | PXD011931 | Pride
Project description:Ascending bacterial infections of the male genitourinary tract by Escherichia coli are an important cause of male infertility. Thus understanding mechanisms by which immunocompetent cells such as testicular macrophages (TM) respond to infection and how bacterial pathogens manipulate defense pathways is of great relevance. Following infection with uropathogenic E. coli (UPEC) whole genome expression profiling revealed induction of the calcium-dependent nuclear factor of activated T cells (NFAT) signaling pathway in TM as well as in peritoneal macrophages (PM) that were used in comparison. UPEC-dependent NFAT activation was confirmed in cultured TM and in TM using an in vivo infection model. Elevated expression of NFATC2-regulated anti-inflammatory cytokines was found in TM (IL-4, IL-13) and PM (IL-3, IL-4, IL-13). NFATC2 is activated by a rapid influx of calcium caused by the UPEC pore forming toxin alpha-hemolysin. Mutant analysis identified alpha-hemolysin as the main virulent factor responsible for UPEC-dependant suppression of IL-6 and TNF-a cytokine release from PM. Alpha-hemolysin caused differential activation of MAP kinase and AP-1 signaling pathways in TM and PM leading to differential expression profiles of key pro-inflammatory cytokines in PM (IL-1a, IL-1b and IL-6 downregulated) and TM (IL-1b and IL-6 upregulated). In contrast to PM, treatment with lipopolysaccharide did not result in activation of the NFkB pathway in TM as shown by lack of degradation of IkBa and lack of pro-inflammatory cytokine secretion (IL-6, TNF-a). In conclusion, these results propose a mechanism how TM can defend against microbes, while at the same time they are able to maintain the immune privileged status of the testis. 2 Macrophage populations ( peritoneal, testicular) infected with UPEC CFT073; timepoints of mrna harvest at 0 min (control), 30 min and 60 min; of each point 2 biological replicates; of each repliccate 2 technical replicates: summa summarum: 2*((1+1+1)*2*2)=24 samples
2010-10-20 | E-GEOD-24780 | biostudies-arrayexpress
Project description:Diastolic dysfunction in the aged population is multifactorial. Common features of the aging heart are dysregulated metabolism, elevated oxidative stress, inflammation and fibrosis, where each of these conditions can linked together and further promote the altered phenotype. It becomes increasingly apparent that aged male and female hearts are phenotypically different and these basic differences dictate their responses to treatments such as a response to antioxidants. We used Glycine and N-Acetyl-Cysteine (GlyNAC, precursors of glutathione)- supplemented diet to monitor its effect on cardiac function and exercise performance. We found that this pharmacological intervention was beneficial for male but not female aged mice and the small but significant changes were observed not only on cardiac functions but also on molecular levels where fatty acid metabolism was improved and cardiac matrix stiffness was reduced.
2024-11-05 | PXD048895 | Pride
Project description:Acute myeloid leukemia (AML) is a heterogenous and complex blood cancer, with poor prognosis and wide-raging complications. Early identification and prediction of complications is vital for effective disease management. We performed longitudinal plasma profiling of 26 AML patients during chemotherapy-induced neutropenia, to explore the role of plasma proteins in evaluating the severity and prognosis of AML. We found that the majority of proteins varied in levels between patients, while remaining relatively stable within patients. Inflammatory proteins were significantly correlated with fever and its complications, and may serve as a useful biomarker panel to monitor AML patients during disease progression.
2024-11-06 | PXD040526 | Pride
Project description:Blood donation is generally considered to be safe, however to ensure blood donor health it is important to monitor the impact of a whole blood donation. Study design and methods Here, we used quantitative mass spectrometry to assess the global plasma proteomic impact of longitudinal whole blood donation in 5 new and 4 regular donors over a period of 180 days as well as the effect on iron status, by selecting 78 donors based on high levels of ferritin and hemoglobin. The majority of plasma proteins were stable between whole blood donors and demonstrated a low coefficient of variation, irrespective to iron status or donors status (new or regular). Longitudinal analysis showed limited differences between the plasma proteomes of regular and new upon a whole blood donation, apart from a consistent and significant short-term decrease in fibronectin. Plasma protein levels measured with MS highly correlated with blood count and lipid parameters, validating our MS-approach. Based on protein co-expression, we observed protein complexes of diverse biological processes, platelet and neutrophil signatures, complement and immune responses with a highly correlating cluster of IGHM, IGJ and CD5L. We showed higher inter- than intra-individual variation, most notably of immunoglobulins and allelic variants for alpha-1 antitrypsin. Overall, this study shows that whole blood donation has limited impact for both new and regular donors apart from short-term decreases in fibronectin and that varying iron statuses do not affect the global plasma proteome. We showed that individual specific signatures were reflected on the plasma proteome as well as detection of allelic variants
2023-02-01 | PXD035447 | Pride