Photoaffinity for Puerarin and mouse brainstem
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): Brain
SUBMITTER: 
Qianqian Lyu
LAB HEAD: Jiqiu Wang
PROVIDER: PXD052140 | Pride | 2024-09-06
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Comp_01.raw | Raw | |||
| Comp_02.raw | Raw | |||
| Comp_02.zip | Other | |||
| Comp_03.raw | Raw | |||
| Comp_03.zip | Other |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Emerging evidence indicates that metabolic enzymes perform moonlighting functions during tumor progression, including the modulation of chemoresistance. However, the underlying mechanisms of these functions remain elusive. In this study, utilizing a metabolic CRISPR-Cas9 knockout library screen, we observed that loss of Glutamate-cysteine ligase modifier subunit (GCLM), a rate-limiting enzyme in glutathione biosynthesis, noticeably heightens the sensitivity of colorectal cancer (CRC) cells to platinum-based chemotherapy. Mechanistically, we unveil a noncanonical mechanism through which nuclear GCLM competitively interacts with NF-kappa-B-repressing factor (NKRF), a known inhibitor of NF-κB signaling, to promote NF-κB activity and subsequently facilitate chemoresistance. In response to platinum drug treatment, P38 MAPK phosphorylates GCLM at T17, resulting in its recognition by importin a5 and subsequent nuclear translocation. Furthermore, elevated expression of nuclear GCLM correlates with unfavorable prognosis and poor benefit from standard chemotherapy. Overall, our work shed light on the essential nonmetabolic role and posttranslational regulatory mechanism of GCLM in enhancing NF-κB activity and subsequent chemoresistance.
2024-11-15 | PXD055376 | Pride
Project description:Foodcrusts are often discovered inside archaeological pottery and other containers. They can provide abundant information about vessel function, diet, cuisine activities and human subsistence strategies. Lipid analysis has been used for decades to characterize foodcrusts, indicating their compositions and biological sources. Recently, proteomics has also been applied to foodcrusts, providing more specific information about the tissues and species origins. In this study, lipid and proteomic analysis were combined to analyze foodcrusts in pottery from the Xiawan site of the Taihu Lake region, East China. These pottery sherds are mainly attributed to the Songze cultural period (ca. 5800-5300 BP). The results show that these foodcrusts contain interpretable concentrations of lipid compounds, including a series of common medium- and long-chain fatty acids, dicarboxylic acids, aliphatic alcohols, sterols and their derivatives, isoprenoid fatty acids and long-chain ketones, as well as proteins of terrestrial mammals and aquatic products. This study provides direct evidence for the function of pottery and the exploitation of animal and plant resources at that time, especially freshwater products, marine fish, rice and millet. Therefore, the combination of lipid and proteomic analysis has great potential in organic residue analysis for foodcrusts.
2025-07-10 | PXD046696 | Pride
Project description:Foodcrusts are often discovered inside archaeological pottery and other containers. They can provide abundant information about vessel function, diet, cuisine activities and human subsistence strategies. Lipid analysis has been used for decades to characterize foodcrusts, indicating their compositions and biological sources. Recently, proteomics has also been applied to foodcrusts, providing more specific information about the tissues and species origins. In this study, lipid and proteomic analysis were combined to analyze foodcrusts in pottery from the Xiawan site of the Taihu Lake region, East China. These pottery sherds are mainly attributed to the Songze cultural period (ca. 5800-5300 BP). The results show that these foodcrusts contain interpretable concentrations of lipid compounds, including a series of common medium- and long-chain fatty acids, dicarboxylic acids, aliphatic alcohols, sterols and their derivatives, isoprenoid fatty acids and long-chain ketones, as well as proteins of terrestrial mammals and aquatic products. This study provides direct evidence for the function of pottery and the exploitation of animal and plant resources at that time, especially freshwater products, marine fish, rice and millet. In addition, as an indicator of high-temperature heating, long-chain ketones may have the potential to be used for prescreening the preservation of ancient proteins in foodcrusts. Therefore, the combination of lipid and proteomic analysis has great potential in organic residue analysis for foodcrusts.
2025-07-10 | PXD045813 | Pride
Project description:Posttranslational modification of proteins by N-linked glycosylation is crucial for many life processes. However, the exact contribution of N-glycosylation to mammalian female reproduction remains largely undefined. Here, DPAGT1, the enzyme that catalyzes the first step of protein N-glycosyation, is identified to be indispensable for oocyte development in mice. A recessive missense mutation (c. 497A>G; p. Asp166Gly) of Dpagt1 causes female subfertility without grossly affecting other functions. Mutant females ovulate fewer eggs owing to defects of follicular development beyond the late secondary stage. Oocytes ovulated by mutants carry a thin and fragile zona pellucida, and display poor developmental competence after fertilization in vitro. Moreover, completion of the first meiosis is accelerated in mutant oocytes, which is coincident with the elevation of aneuploidy. Mechanistically, transcriptomic analysis reveals the downregulation of a number of transcripts essential for oocyte meiotic progression and preimplantation development (e.g., Pttgt1, Esco2, Orc6, and Npm2) in mutant oocytes, which could account for the defects observed. Furthermore, conditional knockout (CKO) of Dpagt1 in oocytes recapitulates the phenotypes observed in Dpagt1 mutant females, and causes complete infertility. Taken together, these data indicate that protein N-glycosylation in oocytes is essential for female fertility in mammals by specific control of oocyte development.
2021-09-09 | PXD018531 | Pride
Project description:Cancer stem cells (CSCs) play crucial roles in cancer progression, immune evasion, drug resistance, and recurrence. Understanding the mechanisms behind CSCs generation and stemness maintenance is vital for early cancer diagnosis and treatment. Here, we unveil that carnitine palmitoyltransferase 1A (CPT1A) is highly expressed in ovarian cancer stem cells (OCSCs) and is essential for maintaining stemness by regulating lipid desaturation. Studies confirmed that CPT1A enhances SREBP1 activation, upregulating SCD1 expression, and promoting lipid desaturation in OCSCs. Mechanistic studies reveal that CPT1A promotes succinylation of mitochondrial fission factor (MFF) through its lysine succinyltransferase (LSTase) activity, crucial for mitochondria-associated membranes formation and SREBP1 activation. Inhibiting CPT1A's LSTase activity with Glyburide reduces OCSCs' stemness and enhances cisplatin's anti-tumor effects against ovarian cancer in vitro and in vivo. Together, our studies highlight the significance of CPT1A's LSTase activity in maintaining OCSCs' stemness, offering potential targets and therapeutic strategies for ovarian cancer treatment.
2025-05-07 | PXD059026 | Pride
Project description:In this study, roots of Rehmannia glutinosa were used as experimental material, and three tuber roots of Rehmannia glutinosa in extension stage (I), expansion stage (E) and mature stage (M) were selected as samples, The iTRAQ quantitative proteomic technology combined with two-dimensional liquid chromatography and tandem mass spectrometry (2D-LC-MSMS) technology was used to construct the root tuber proteome database of Rehmannia glutinosa, the genes related to the growth and development of Rehmannia glutinosa root tuber were found.
2022-02-17 | PXD025914 | Pride
Project description:Protein reference databases are a critical part of producing efficient proteomic analyses. However, the method for constructing clean, efficient, and comprehensive protein reference databases is lacking. Existing methods either do not have contamination control procedures, or these methods rely on a three-frame and/or six-frame translation that sharply increases the search space and harms MS results. Herein we propose a framework for constructing a customized comprehensive proteomic reference database (CCPRD) from draft genomes and deep sequencing transcriptomes. Its effectiveness is demonstrated by incorporating the proteomes of nematocysts from endoparasitic cnidarian: myxozoans. By applying customized contamination removal procedures, contaminations in omic data were successfully identified and removed. This is an effective method that does not result in over-decontamination. This can be shown by comparing the CCPRD MS results with an artificially-contaminated database and another database with removed contaminations in genomes and transcriptomes added back. CCPRD outperformed traditional frame-based methods by identifying 35.2%-50.7% more peptides and 35.8%-43.8% more proteins, with a maximum 84.6% in size reduction. A BUSCO analysis showed that the CCPRD maintained a relatively high level of completeness compared to traditional methods. These results confirm the superiority of the CCPRD over existing methods in peptide and protein identification numbers, database size, and completeness. By providing a general framework for generating the reference database, the CCPRD, which does not need a high-quality genome, can potentially be applied to any organisms and significantly contribute to proteomic research.
2020-07-09 | PXD018851 | Pride
Project description:Breast cancer (BC) is an important disease with high incidence as well as mortality among women, and critical socio-economic impacts. In the past 50 years, it has become a major health problem for women worldwide with over 2 million new cases diagnosed in 2018. This represents about 12% of all new cancer cases, 25% of all cancers in women and more than 600.000 cases of deaths worldwide in 2018 (Bray et al, 2018). If the cancer is located only in the breast, the 5-year relative survival rate of people with BC is 99% but this rate decreases if it is spread to lymph nodes (85%) and more dramatically if diagnosed with distant metastasis (26%) (Howlader et al, 2019; Siegel et al, 2017). Metastatic process, or the spread of tumor cells throughout the body, is responsible for about 90% of cancer patient deaths (Chaffer et al, 2011) and represents the central clinical challenge of solid tumor oncology. The development and progression of BC are complex processes that involve hormonal factors as well as numerous genetic and epigenetic alterations. During the past 10 years, many studies have focused on the role of the tumor microenvironment and the peritumoral stromal fraction, composed of adipose tissue, cancer-associated fibroblasts, endothelial cells and immune cells as macrophages and leukocytes. During tumor progression, cancer cells will deeply modify their microenvironment which in return will promote the growth and dissemination of the tumor (Allen et al, 2011; Polanska et al, 2013). Adipose tissue, consisting of mainly mature adipocytes and progenitors (preadipocytes and adipose-derived stem cells (ADSCs), is the most abundant component surrounding BC cells. Adipose tissue exerts a major endocrine and secretory role, and represents then an essential actor in the inflammatory, angiogenic or remodeling responses of the extracellular matrix, which influences tumor behavior.
2021-02-09 | PXD014328 | Pride
Project description:Cancers with activating mutations of KRAS show a high prevalence and poor prognosis but remain intractable, requiring innovative strategies to overcome the poor targetability of KRAS. Here, we report that KRAS expression was post-translationally up-regulated through the deubiquitination of KRAS protein when the scaffolding function of NDRG3 (N-Myc downstream regulated gene 3) promoted specific interaction between KRAS and a deubiquitinating enzyme, USP9X. In KRAS-mutant pancreatic or lung cancer cells KRAS protein expression, downstream signaling, and cell growth were highly dependent on NDRG3. In conditional KrasG12D knock-in mouse models of pancreatic ductal adenocarcinoma (PDAC), Ndrg3 depletion abolished Kras protein expression in pancreas, and suppressed pancreatic intraepithelial neoplasia (PanIN) formation. Mechanistically, KRAS protein bound to the C-terminal serine/threonine-rich region of NDRG3, subsequently going through the deubiquitination by USP9X recruited to the complex. This interaction could be disrupted in a dominant-negative manner by a C-terminal NDRG3 fragment that can bind KRAS but is defective in USP9X binding, highly suppressing the KRAS protein expression and KRAS-driven cell growth. In summary, KRAS-driven cancer development critically depends on the deubiquitination of KRAS protein mediated by USP9X/NDRG3, and KRAS-addicted cancers could be effectively targeted by inhibiting the KRAS-NDRG3 interaction.
2025-05-07 | PXD052379 | Pride
Project description:Haemonchus contortus has developed complexed and multifaceted mechanisms of immune evasion to enable the survival in the host. Generating excretion and secretion products (ESPs) to subvert or suppress the functions of host cytokines is a newly immune regulatory pattern found during recent years. TGF-β1 has critical immune regulatory functions in nematode infections. In this study, the co-immunoprecipitation was used to collect the molecules which bound to the goat TGF-β1 from ESPs, and the precipitates were identified by mass spectrometry using shotgun LC-MS / MS.
2020-09-08 | PXD020699 | Pride