Human Lung Adenocarcinoma Cells: control vs. mAb NJ001 treated
Ontology highlight
ABSTRACT: Transcriptional profiling of human lung adenocarcinoma cells comparing control untreated SPC-A1 cells with SPC-A1 cells treated with 300 M-BM-5g/ml mAb NJ001 for 36h Two-condition experiment, SPC-A1 vs. NJ001-SPC-A1 cells. Biological replicates: 3 control, 3 treated, independently grown and harvested. One replicate per array.
Project description:Transcriptional profiling of human lung adenocarcinoma cells comparing control untreated SPC-A1 cells with SPC-A1 cells treated with 300 µg/ml mAb NJ001 for 36h
Project description:Sacha Inchi (Plukenetia volubilis) oil press-cake (SIPC) represents a new source of proteins of high biological value, with promissory food applications. However, knowledge of these proteins remains limited. In this study, a Sacha Inchi protein concentrate (SPC) was extracted from the SIPC, and proteomic analysis was performed to identify the major alkaline-soluble proteins. Electrophoretic profiles highlighted the efficacy of conditions to extract the major proteins, from which five proteins, not previously reported, were registered. LC-MS/MS analyses produced abundant high-quality fragmentation spectra. Utilizing the Euphorbiaceae database (DB), 226 proteins were identified, with numerous well-assigned spectra remaining unidentified. The PEAKS Studio software generated high quality de novo peptides. Gene ontology (GO) classification allowed the identification of sequenced proteins associated with biological processes, molecular functions, and cellular components. The main alkali-soluble proteins from SPC were characterized by the derived functional analysis like seed storage, defense-related, and carbohydrate and lipid metabolism-related proteins. These results contribute to the information of the emerging proteomic studies on Sacha Inchi.
Project description:Sphingosylphosphorylcholine (SPC) is a bioactive lipid with multiple biological roles including the regulation of differentiation in embryonic and cancer cells. PaTu II pancreatic cancer cells were incubated with 15 μM SPC in serum-free Medium for 2 h or left untreated. Duplicates of 3 independent experiments were analyzed.
Project description:The ER-resident signal peptidase complex (SPC) is an essential membrane protein complex involved in the maturation of soluble and type-I transmembrane proteins destined to the secretory pathway. As a part of the ER translocon machinery, the SPC removes signal peptides (SPs) from the N-termini of many proteins such as hormones, antibodies, or secretory enzymes1,2. To accomplish this task, the SPC must process a large variety of SPs with an exquisite specificity. Although the determinants of SP recognition have been established empirically3, the molecular details of SP recognition and removal remain elusive. Here, we show that the human SPC exists in two functional paralogs with distinct proteolytic subunits. We determined the structures and posttranslational modifications of both paralogs using electron cryo-microscopy and structural proteomics. The respective proteolytic subunits SEC11A and SEC11C adopt a conserved signal peptidase (SPase) fold with their active sites facing a prominent transmembrane window, which is collectively formed by the transmembrane domains of all SPC subunits. Characteristic, charged regions on both sides of this window locally thin the membrane by approximately 40% compared to the exterior. The data suggest a mechanistic model for SPC specificity and the transfer of SPs from the Sec61 translocation channel to the SPC.
Project description:To define the role of MAGE-A1 in melanoma growth and metastasis, we performed RNA-seq analysis on MAGE-A1 overexpression (OE) and knockdown (KD) models in A375 human melanoma cell line. Our results revealed that overexpression of MAGE-A1 dramatically promoted proliferation, migration, and invasion of human melanoma cells in vitro and down-regulated of MAGE-A1 inhibited tumor cell proliferation and invasion. Furthermore, MAGE-A1 exerts its tumor promoting activity via activating including ERK-MAPK signaling pathway by RNA-seq analysis. mRNA profiles of MAGE-A1 over expression (OE), knockdown (KD), pcDNA-vector control, and pRNAT-scramble control in A375 cell line were generated using Ion torrent
Project description:SP100030 and SPC-839 are structurally distinct molecules sharing similar cellular activity profiles. We used click chemistry-mediated chemoproteomics to identfy candidate mechanistic targets for these small molecules.
Project description:The hnRNP A1 and A2 proteins regulate processes such as alternative pre-mRNA splicing and mRNA stability. Here, we report that a reduction in the levels of hnRNP A1 and A2 by RNA interference or their cytoplasmic retention by osmotic stress drastically increases the transcription of a reporter gene. Based on previous work, we propose that this effect may be linked to a decrease in the activity of the transcription elongation factor P-TEFb. Consistent with this hypothesis, the transcription of the reporter gene was stimulated when the catalytic component of P-TEFb, CDK9, was inhibited with DRB. While low levels of A1/A2 stimulated the association of RNA polymerase II with the reporter gene, they also increased the association of CDK9 with the repressor 7SK RNA, and compromised the recovery of promoter-distal transcription on the Kitlg gene after the release of pausing. Transcriptome analysis revealed that more than 50% of the genes whose expression was affected by the siRNA-mediated depletion of A1/A2 were also affected by DRB. RNA polymerase II-chromatin immunoprecipitation assays on DRB-treated and A1/A2-depleted cells identified a common set of repressed genes displaying increased occupancy of polymerases at promoter-proximal locations, consistent with pausing. Overall, our results suggest that lowering the levels of hnRNP A1/A2 elicits defective transcription elongation on a fraction of P-TEFb-dependent genes, hence favoring the transcription of P-TEFb-independent genes. two treatements and one control
Project description:This experiment identifies hnRNP A1 binding sites transcriptome-wide in Hela cells. HeLa cells with inducible expression of T7-tagged hnRNP A1 were grown to approximately 90% confluence and then subject to iCLIP analysis (following the protocol from Huppertz et al. 2014 (iCLIP: protein-RNA interactions at nucleotide resolution)). The iCLIP library was sequenced using Illumina's HighSeq 1500
Project description:The macrophage-Brucella interaction is critical for the establishment of a chronic Brucella infection. Smooth virulent B. suis strain 1330 (S1330) prevents macrophage cell death. However, rough attenuated B. suis strain VTRS1 induces strong macrophage cell death. To further investigate the mechanism of VTRS1-induced macrophage cell death, microarrays were used to analyze temporal transcriptional responses of murine macrophage-like J774. A1 cells infected with S1330 or VTRS1. Murine J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 or VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 0, 1, 2, 4, 8, 24, and 48 h post infection. The RNA samples were stored at -80 ºC until an Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) was used to assess the concentrations and quality of RNA samples. Total RNA (20 µg) per sample was used for hybridization with Affymetrix mouse GeneChip 430 2.0 array. Preparation of cDNA, hybridization, quality controls and scanning of the GeneChip 430 2.0 arrays were performed according to the manufacturer's protocol (Affymetrix, Santa Clara, CA) .
Project description:Investigation of whole genome gene expression level changes in Sphingomonas. sp A1 AlgO-deficient mutant grown on alginate compared with that on yeast extract AlgO is a possble transcriptional factor described in J. Bacteriol. (2000) 182(14):3998-4004 by Momma K, Okamoto M, Mishima Y, Mori S, Hashimoto W, and Murata K. A two chip study using total RNA recovered from two cultures of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium and 0.5% yeast extract medium. Each chip measures the expression level of genes from Sphingomonas. sp A1.