Cysteine profiling by CL26-alkyne to investigate protein targets of CL26 in MHCC97L cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Hepatocyte
DISEASE(S): Liver Cancer
SUBMITTER: 
Tin Yan Koo
LAB HEAD: CHUNG, Clive Yik Sham
PROVIDER: PXD057704 | Pride | 2025-07-21
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 97L_CL26-alkyne_Tryptic-digest_MaxQuant-Output.zip | Other | |||
| 97L_CL26-alkyne_Tryptic-digest_mqpar.xml | Xml | |||
| 97L_DMSO1.d.zip | Other | |||
| 97L_DMSO2.d.zip | Other | |||
| 97L_DMSO3.d.zip | Other |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:We have identified CL26 as a covalent inhibitor against AGPAT4, an aberrant protein complicated in hepatocellular carcinoma (HCC). CL26 treatment reversed HCC stemness and resistance to the first-line medication sorafenib. This experiment was conducted to investigate the protein targets of CL26 in Huh7 cells.
2025-07-21 | PXD057706 | Pride
Project description:We have identified CL26 as a covalent inhibitor against AGPAT4, an aberrant protein complicated in hepatocellular carcinoma (HCC). CL26 treatment reversed HCC stemness and resistance to the first-line medication sorafenib. This experiment was conducted to investigate the covalent binding of CL26 onto AGPAT4 in vitro.
2025-07-21 | PXD057674 | Pride
Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.
2015-03-06 | E-GEOD-59792 | biostudies-arrayexpress
Project description:AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC). The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Series 1: Growth conditions: Sterilized seeds will be stratified at 4degreeC for 3 days, exposed to white light for 2 h to induce germination, and grown on MS agar plates (0.9 % agar) without sugar in total darkness for 4 days at 22degreeC. Seedlings will then be transferred to the light conditions described for each slide below for 1 h (to identify early induced genes) and 4 hrs (maximum expression of the first initial light response of most target genes), respectively. All light treatments will be done in parallel to minimize the number of dark controls. All samples will be done in triplicate and only with shoots. Experimenter name = Thomas Kretsch; Experimenter institute = AtGenExpress Experiment Overall Design: 48 samples were used in this experiment
2008-06-13 | E-GEOD-5617 | biostudies-arrayexpress
Project description:We profiled miRNA expression in tissue samples (104 HCC, 90 adjacent cirrhotic livers, 21 normal livers) as well as in 35 HCC cell lines. A set of 12 miRNAs (including miR-21, miR-221/222, miR-34a, miR-519a, miR-93,miR-96, and let-7c) was linked to disease progression from normal liver through cirrhosis to full-blown HCC. miR-221/222, the most upregulated miRNAs in tumor samples, are shown to target the CDK inhibitor p27 and to enhance cell growth in vitro. Conversely, these activities can be efficiently inhibited by an antagomiR specific for miR-221. In addition, we show, using a mouse model of liver cancer, that miR-221 overexpression stimulates growth of tumorigenic murine hepatic progenitor cells.
2009-12-08 | E-TABM-866 | biostudies-arrayexpress
Project description:In this study we investigated the miRNA expression profile of Hepatocellular carcinoma (HCC) specimens from radical resection. We developed a unique 20 miRNA signature that could significantly distinguish HCC venous metastasis from metastasis-free HCC. In contrast to HCC staging systems, this signature was capable of predicting survival and recurrence of HCC patients with multinodular or solitary tumors, including those with early-stage disease. Moreover, the signature was an independent and significant predictor of patient prognosis and relapse when compared to other available clinical parameters. Our study suggests that these 20 miRNAs can enable HCC prognosis and may have clinical utility for the advance identification of HCC patients with a propensity towards metastasis/recurrence. Keywords: disease state design Gene expression profiles were conducted in primary HCC and corresponding noncancerous hepatic tissues from 244 Chinese HCC patients. A total of 134 well-defined cases were used as a training group. Among them, 30 had primary HCC lesions accompanied by tumor emboli and 104 had solitary HCC with no metastasis/recurrence found at follow-up (3 yr). We used a testing group of 110 independent cases. The testing cases included 43 multinodular and 67 solitary HCC. In addition, eight normal liver tissues from disease-free patients were included as normal controls. In the analysis of the 244 HCC cases, RNA was isolated in a pairwise fashion from tumor or non-tumor tissue and samples were selected in random order for miRNA analysis to avoid grouping bias.
2008-01-14 | E-GEOD-6857 | biostudies-arrayexpress
Project description:Myristic acid, the 14-carbon saturated fatty acid (C14:0), is usually associated with negative consequences for human health, and in particular its consumption is correlated to an increased cardiovascular disease risk. Since it is a little abundant into the cells, its specific properties and functional roles have not been fully described. The aim of this study was to explore the cell response to this fatty acid to help explaining clinical findings on the relationship between C14:0 and cardiovascular disease. Primary murine hepatocytes were used as a model to investigate the hepatic response to C14:0 in a proteomic approach. C14:0 treatment (250 µM) of primary murine hepatocytes confirmed that myristic acid induces lipid droplet accumulation as shown by cellular imaging and elevated perilipin 2 levels on cellular proteome level. The functionally enriched pathways were involved in protein synthesis, transport and degradation, protein depalmitoylation, unfolded protein response, lipid and cholesterol metabolism, mitophagy in response to depolarization, and cell cell adhesion. Our data provide for the first time quantitative proteomic data regarding C14:0 in primary murine hepatocytes (M1 in present dataset) and contribute to the elucidation of the molecular mechanisms through which this fatty acid can cause adverse health effects.
2022-03-01 | PXD009017 | Pride
Project description:Due to the common presence of a non-virion NV gene absent from other fish rhabdoviruses, NV-coding rhabdoviruses, such as the viral haemorrhagic septicemia (VHSV), were placed into a new Novirhabdovirus genus. Because conflicting results do exist on the importance of NV for VHSV trout pathogenicity and the NV function is still unclear, the effects of intraperitoneal injection of recombinant NV protein were studied by using home-designed immune-related microarrays from rainbow trout Oncorhynchus mykiss. Trouts were separated in two groups. One group was injected with PBS and it was used as control group. Second group was injected with soluble VHSV non-virion (NV) recombinant protein
2014-05-05 | E-GEOD-37797 | biostudies-arrayexpress
Project description:Major advances have been made to improve the sensitivity of mass analyzers, spectral quality, and the speed of data processing enabling more comprehensive proteome discovery and quantitation. While focus has recently begun shifting toward robust proteomic sample preparation efforts, a high throughput proteomics sample preparation is still lacking. We report the development of a highly-automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. Digestion efficiency was excellent in comparison to a commercial digest peptide standard with minimal sample loss while improving sample preparation throughput by 20- to 40-fold (<1 min/sample for entire process from cells to clean peptides). Analysis of six human cell types, which included two primary cell samples, identified and quantified approximately 4,000 proteins for each sample in a single HPLC-MS/MS injection with only 100 -10,000 cells, thus demonstrating universality of the platform.
2021-06-14 | PXD023374 | Pride
Project description:Due to the common presence of a non-virion NV gene absent from other fish rhabdoviruses, NV-coding rhabdoviruses, such as the viral haemorrhagic septicemia (VHSV), were placed into a new Novirhabdovirus genus. Because conflicting results do exist on the importance of NV for VHSV trout pathogenicity and the NV function is still unclear, the effects of intraperitoneal injection of recombinant NV protein were studied by using home-designed immune-related microarrays from rainbow trout Oncorhynchus mykiss. The results were compared with parallel experiments using bacterial flagellins, a well know mammalian agonist of toll receptors (tlr5) with adjuvant activity recently described also in fish Four experimental groups were formed with four biological replicates each, 16 samples in total. First one was injected with NV recombinant protein in PBS, second one was a control group injected with PBS, the third group was injected with bacterial flagellins in PBS and the fourth group was injected with polihistidine peptide as a reference group because the recombinant proteins have a polihistidine tail. There is a technical replicate within each array.
2014-08-11 | E-GEOD-31557 | biostudies-arrayexpress