TMT-labelled quantitative proteomics of 9 grape skin tissue samples
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Vitis Vinifera (grape)
TISSUE(S): Skin
SUBMITTER: 
Jane Jing
LAB HEAD: Jiao Feng
PROVIDER: PXD042532 | Pride | 2024-01-17
REPOSITORIES: Pride
Similar Datasets
Project description:Extracellular pH (pHe) is lower in many tumors than in the corresponding normal tissue. Acidic tumor microenvironment has been shown to facilitate epithelial mesenchymal transition (EMT) and tumor metastasis, while the mechanisms underlying tumor acidic microenvironment-induced tumor cell metastasis remain undefined. Here, we aimed to investigate the tumor metastasis and the EMT by acidic microenvironment and to explore their mechanisms and clinical significance in lung cancer. Results showed that acidic pHe remarkably enhanced invasion ability of lung cells accompanying with increased mesenchymal and decreased epithelial markers. Moreover, acidic pHe triggered the inhibition of microRNA-7 (miR-7) expression and activation of TGF-β2/SMAD signaling. Mechanistic studies showed that TGF-β2 is a direct potential target gene of miR-7, and acidity-induced metastasis could be abolished by treatment with a TGFβRI inhibitor, anti-TGF-β2 antibody and miR-7 mimic, respectively. The clinical samples further revealed that miR-7 was decreased in lung tissues and antagonistically correlated with TGF-β2 expression, associating with overall survival and metastasis. In conclusion, our study indicated that acidic pHe showed enhanced invasive potential, and enhanced potential to develop experimental metastases by a novel mechanism involving tumor acidic microenvironment-induced regulation of miR-7/TGF-β2/SMAD axis. Our findings suggest that the possibility that pHe of the primary tumor may be an important prognostic parameter for lung cancer patients merit clinical investigation. Moreover, miR-7 may serve as prognostic molecular marker and a novel therapeutic target for lung cancer.
2022-04-01 | PXD016524 | Pride
Project description:Long term chest blast exposure can lead to mental disorders, brain inflammation and oxidative stress in soldiers. However, the underlying mechanism of brain injury caused indirectly by chest blast remains unclear. It is urgent to find more potential biomarkers to reveal the deeper pathogenesis of this phenomenon. We used iTRAQ labeling combined with LC-MS/MS to screen potential differentially expressed proteins in rat brain after chest blast at different time points. Meanwhile, we also used Go, KEGG, David and Cytoscape to analyze the proteomic profile and explore its pathogenesis. Moreover, Western blotting was used to verify the target proteins. Our data showed that, a total of 6,931 proteins were identified. A total of 255 differentially expressed proteins were identified, of which 43, 84, 52, 97 and 49 proteins were identified from brain tissues at 12h, 24h, 48h, 72h, and 1w after chest blast exposure. Bioinformatics analysis, including GO, COG, KEGG and STRING, further proved that brain damage caused by chest blast exposure was involved in many important biological processes and signal pathways, such as inflammation, cell adhesion, phagocytosis, neuronal and synaptic damage, oxidative stress and apoptosis. Moreover, Western blotting further confirmed that these differentially expressed proteins and signaling pathways were associated with brain damage caused by chest blast exposure. For the first time, we screened and verified the potential protein biomarkers of brain damage caused indirectly by chest blast, and provided a new target for the treatment of this disease.
2021-12-30 | PXD025204 | Pride
Project description:Ionizing irradiation kills pathogens by destroying nucleic acids while retaining the immunogenicity of pathogen proteins. However, the overall proteome of bacteria exposed to X-ray irradiation still remain unclear. This experiment was aimed to investigate the proteome changes of the laboratory Pseudomonas aeruginosa PAO1 strain after exposure to X-ray irradiation. A total of 2963 proteins were identified in this study, of which 2599 proteins contained quantitative information. If the differential expression change threshold is 2 times, and the statistical test t-test p-value <0.05 is the significance threshold, then among the quantified proteins, the expression of 48 proteins was up-regulated and 8 protein expression was down-regulated. Based on the above data, we performed a systematic bioinformatics analysis of all identified proteins, and performed functional classification, functional enrichment, and clustering analysis based on functional enrichment for all differentially expressed proteins. Combined with the above information, it provides a reference direction for further investigation in the biological effect on P. aeruginosa PAO1 and its MV formation under X-ray irradiation.
2020-12-14 | PXD019035 | Pride
Project description:Quantitative acetyl-proteomics, a newly identified post-translational modification, is known to regulate transcriptional activity in different organisms. Neurospora crassa is a model ascomycete fungus maintained for biochemistry and molecular biology research; however, extensive studies of the functions of its acylation proteins have yet to be performed. In this study, using LC-MS/MS qualitative proteomics strategies, we identified 1909 modification sites on 940 proteins in N. crassa and analysed the functions of these proteins using GO enrichment, KEGG pathway, and subcellular location experiments. We classified the acetylation protein involvement in diverse pathways, and protein-protein interaction (PPI) network analysis further demonstrated that these proteins participate in diverse biological processes. In summary, our study comprehensively profiles the crosstalk of modified sites, and PPI among these proteins may form a complex network with both similar and distinct regulatory mechanisms, providing improved understanding of their biological functions in N. crassa.
2021-01-26 | PXD022001 | Pride
Project description:Background: Autosomal dominant osteopetrosis type II (ADO2) is a rare human genetic disease that has been broadly studied as an important osteopetrosis model; however, there are no disease-specific induced pluripotent stem cells (ADO2-iPSCs) that may be valuable for understanding the pathogenesis and may be a potential source of cells for autologous cell therapy. Methods: To generate the first human ADO2-iPSCs from a Chinese family with ADO2 and to identify their characteristics, blood samples were collected from the proband and his parents and were used for genotyping by whole-exome sequencing (WES); the urine-derived cells of the proband were reprogrammed with episomal plasmids that contained transcription factors, such as KLF4, OCT4, c-MYC, and SOX2. The proteome-wide analysis of lysine 2-hydroxyisobutyrylation in the ADO2-iPSCs and control cell lines was performed by high-resolution LC-MS/MS and a bioinformatics analysis. Results: WES with filtering strategies identified a mutation in CLCN7 (R286W) in the proband and his father, which was absent in the proband’s mother and the healthy controls; this was confirmed by Sanger sequencing. The ADO2-iPSCs were successfully generated, which carried the normal male karyotype (46, XY) and carried the mutation of CLCN7 (R286W); the ADO2-iPSCs positively expressed alkaline phosphatase and other surface markers; and no vector and transgene was detected. The ADO2-iPSCs could differentiate into all three germ cell layers, both in vitro and in vivo. Our proteomic profiling detected 7, 405 proteins and revealed 3,684 2-hydroxyisobutyrylated sites in 1,036 proteins in the ADO2-iPSCs. Conclusions: Our data indicated that mutation CLCN7 (R286W) may be a cause of the osteopetrosis family. The generated vector-free and transgene-free ADO2-iPSCs with identified lysine 2-hydroxyisobutyrylation may be valuable for personalized and cell-based regenerative medicine in the future.
2022-02-15 | PXD014227 | Pride
Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered post-translational modification in some prokaryotic and eukaryotic organisms. Here, we carried out proteome-wide analysis of Khib in Fusarium graminearum, identifying the reshaping of lysine 2-hydroxyisobutyrylome by tebuconazole or carbendazim, using the most recently-developed high-resolution LC-MS/MS in combination with high-specific affinity enrichment. In total, 3035 quantifiable Khib sites on 937 proteins were identified. With the criteria of fold changes over 1.3, normalized with total proteins, 1083 Khib sites of 509 proteins were considered as significantly affected by tebuconazole treatment, while 344 Khib sites of 227 proteins were significantly affacted by carbendazim. Furthermore, bioinformatics analysis were conducted.
2022-04-04 | PXD022499 | Pride
Project description:Background: Sex and age have substantial influence on thyroid function. Sex influences the risk and clinical expression of thyroid disorders (TDs), with age a proposed trigger for the development of TDs. Cardiac function is affected by thyroid hormone levels with gender differences. Accordingly, we investigated the proteomic changes involved in sex based cardiac responses to thyroid dysfunction in elderly mice. Methods: Aged (18-20 months) male and female C57BL/6 mice were fed diets to create euthyroid, hypothyroid, or hyperthyroid states. Serial echocardiographs were performed to assess heart function. Proteomic changes in cardiac protein profiles were assessed by 2-D DIGE and LC-MS/MS, and a subset confirmed by immunoblotting. Results: Serial echocardiographs showed ventricular function remained unchanged regardless of treatment. Heart rate and size increased (hyperthyroid) or decreased (hypothyroid) independent of sex. Pairwise comparison between the six groups identified 55 proteins (≥ 1.5-fold difference and p < 0.1). Compared to same-sex controls 26/55 protein changes were in the female hypothyroid heart, whereas 15/55 protein changes were identified in the male hypothyroid, and male and female hyperthyroid heart. The proteins mapped to oxidative phosphorylation, tissue remodeling and inflammatory response pathways. Conclusion: We identified both predicted and novel proteins with gender specific differential expression in response to thyroid hormone status, providing a catalogue of proteins associated with thyroid dysfunction. Pursuit of these proteins and their involvement in cardiac function will expand our understanding of mechanisms involved in sex-based cardiac response to thyroid dysfunction.
2020-12-23 | PXD022557 | Pride
Project description:Histone lysine crotonylation (Kcr) is a newly discovered protein post-translational modification (PTM), which was detected from yeast to humans and is mainly related with active transcription. With the development of proteomics technologies, high abundance of non-histone proteins modified by Kcr was also found recently. Here, we first report that lysine Kcr also occurs on cytoplasmic and mitochondrial proteins in common wheat (Triticum aestivum L.). We identified 4,696 Lys-acetylated sites on 1,726 proteins which involved in a wide variety of biological processes, such as chromatin-associated processes, Calvin-Benson cycle, glycolysis, protein metabolism and transport, which representing the largest dataset of lysine acylation proteome reported in the plant kingdom. Interestingly, 98 proteins were involved in multiple processes of photosynthesis, suggesting an important role of lysine Kcr in processes. In addition, 21 potentially specific Kcr motifs in wheat were detected. The protein interaction network analysis revealed that diverse interactions are modulated by protein Kcr. The overlap between Kcr and acetylation (Kac) indicated that they may coordinately regulate the function of some proteins in common wheat. Futhermore, comparative analysis indicated that lysine Kcr is conserved between common wheat and Nicotiana tabacum. Taken together, this study provided the first global survey of Kcr in wheat, making a promising starting point for further functional analysis of Kcr in plants.
2023-07-20 | PXD008483 | Pride
Project description:Using single-cell RNA sequencing, spatial transcriptomic and bulk multi-omics, we elaborated a molecular architecture of 3 PLC types, namely hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC) from a high-resolution perspective.
2024-01-26 | PXD044778 | Pride
Project description:The CA-MRSA- or MSSA-infected pus samples of breast abscess were collected for the followed dual-omics studies. For label-free analysis, five CAMRSA and five MSSA samples were used, followed by PRM validation of candidate biomarkers.
2024-01-26 | PXD046678 | Pride