Knockdown of serine protease PRSS23 decreased FGF2 expression in gastric cancer
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ABSTRACT:
PROVIDER: PRJNA842019 | ENA |
REPOSITORIES: ENA
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Project description:Serine proteases dysregulation has been considered to be closely associated with the inflammatory response and tumor progression. As a novel serine protease, the biological function of PRSS23 is rarely studied in cancers. In this study, we explored the biological function of PRSS23 in GC by RNA sequencing. Our data highlights that PRSS23 promotes GC progression by promoting macrophage infiltration via regulating FGF2 expression.
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2024-03-14 | GSE249966 | GEO
Project description:NAL1 (NARROW LEAF 1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, but the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure whose formation is mediated by ATP-containing positively charged pocket at the N-terminal region. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signaling pathways, eventually achieving its pleiotropic physiological function. An elite allele NAL1A originated from wild rice could increase grain yield. Furthermore, the NAL1 homologs in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.
2023-05-09 | GSE207132 | GEO
Project description:Our previous study reported that IGFBP7 plays a role in maintaining mRNA stability of oncogenic lncRNA UBE2CP3 by RNA-RNA interaction. Clinical cohort studies had implied an oncogenic role of IGFBP7 in GC. However, the molecular mechanism of IGFBP7 in driving gastric cancer (GC) progression remains unknown. In this study, clinical analysis based on two independent cohort showed that IGFBP7 was positively associated with poor prognosis and macrophage infiltration in GC. Loss-of-function studies confirmed the oncogenic properties of IGFBP7 in regulating GC cell proliferation and invasion. Mechanismly, IGFBP7 was induced by epithelial-to-mesenchymal transition (EMT) signaling, since its expression was increased by TGF-beta treatment and reduced by overexpression of OVOL2 in GC. RNA sequencing, qRT-PCR, ELISA assay showed that IGFBP7 positively regulating FGF2 expression and secretion. Transcriptome analysis revealed that FGFR1 was downregulated in M1 macrophages but upregulated in M2 macrophages. Exogenous recombinant IGFBP7 protein in macrophages and GC cells further identified that IGFBP7 promotes macrophage polarization towards to a M2/TAM phenotype via FGF2/FGFR1/PI3K/AKT axis. Our finding highlights that IGFBP7 promotes GC by enhancing TAM infiltration through FGF2/FGFR1/PI3K/AKT axis.
2022-07-08 | GSE207373 | GEO
Project description:For over 30 years, serine hydroxamate has been used to chemically stimulate a stringent response in Escherichia coli and other bacteria. These studies have elucidated numerous characteristics of the classical stringent response beyond the simple cellular response to an amino acid shortage, including phospholipid synthesis and protease up-regulation. In this study, the effects of a serine hydroxamate addition on high cell density recombinant E. coli were examined and compared to the effects of recombinant protein production to determine overlaps, as recombinant protein production stress has often been attributed to amino acid shortages. Both the transcriptome and growth characteristics were evaluated and compared. The serine hydroxamate addition profoundly decreased the culture growth rate, whereas, recombinant protein production did not. Conversely, the transcriptome profile of the recombinant E. coli cultures were relatively unaffected by the serine hydroxamate addition, yet recombinant protein production dramatically changed the transcriptome profile. A subset of the classical stringent response genes were effected by the serine hydroxamate addition, whereas, recombinant protein production regulated numerous classical stringent response genes; however, not all. The genes that were regulated by the serine hydroxamate addition include numerous fatty acid synthesis genes, in agreement with altered phospholipids synthesis reports. These results indicate that recombinant protein production and the stringent response have many overlapping responses; however, are far from identical. It was hypothesized that recombinant protein production leads to a stringent response due to the high amino acid synthesis demands related to recombinant protein synthesis. A comparison of the transcriptomes during recombinant protein production and a chemical imposed stringent response would assist with determining what portion of the “metabolic burden” associated with recombinant protein production is due to amino acid shortages. In this study, the transcriptome profiles of recombinant E. coli were examined and compared for the three culture conditions: 1) Normal growth, no external stress; 2) L-serine hydroxamate addition (to mediate a stringent response); and 3) IPTG-induction to produce the recombinant protein chloramphenicol acetyltransferase (CAT). The transcriptome profiles from these three conditions were analyzed using Affymetrix Anti-sense E. coli GeneChip® microarrays. Experiment Overall Design: For the serine hydroxamate fermentations, cells were harvested immediately prior to the serine hydroxamate-addition (Time S0) and 1-hour post serine hydroxamate-addition (Time S1). For the IPTG-induced fermentations, cells were harvested immediately prior to the IPTG-addition (Time S0) and 1-hour post-induction (Time S1). For the uninduced (unstressed) fermentations, cells were harvested at Time S0 and Time S1, for which the timing was synchronized with the serine hydroxamate and IPTG fermentations based on OD for Time S0 and time for Time S1. Each fermentation condition was repeated (two biological replicates). RNA from each biological replicates was purified and processed independently. Three biological replicates were obtained for the control condition (Time S0), since prior the serine hydroxamate- or IPTG- addition all fermentations were replicates. Prior to DNA microarray hybridization, where only two biological replicates existed, one of the processed samples was divided into two technical replicates, resulting in three separate hybridized chips. All Time S1 samples contained three technical replicates from two biological duplicates, whereas the control Time S0 measurement contained three biological replicates.
2009-08-25 | E-GEOD-17506 | biostudies-arrayexpress
Project description:This series includes hES cell samples starved and re-stimulated with FGF2. Controls were FGF2-starved but not re-stimulated. Two independent experiments were carried out (one sample plus control each). Keywords: Growth factor stimulation experiment
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Project description:Decreased serine biosynthesis identifies a subgroup of platinum resistant ovarian cancers and novel actionable metabolic vulnerabilities
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Project description:Determine if transcripts are released by protease treatment Keywords: Comparison of protease treatments
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Project description:Biopsies from 24 gastric adenocarcinomas and adjacent normal gastric mucosa were analyzed for from 24 patients following surgical resection of the tumor. Genome-wide DNA methylation profiling of the tumor and matched non-cancerous mucosa was performed and compared to previously performed gene expression, survival and clinicopathological parametres.
2015-10-31 | E-MTAB-3813 | biostudies-arrayexpress