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Transcriptome-wide analysis of the effects of systematic knock down of splicing factors and regulators using siRNAs in HeLa cells

ABSTRACT: Whole proteome analysis upon knock-down of 9 SF/RBP and control condition in HeLa cells.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Juan Valcarcel

LAB HEAD: Juan Valcárcel Juárez

PROVIDER: PXD054242 | Pride | 2024-11-08

REPOSITORIES: Pride

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			Action	DRS
	2024MK013_SOBO_001_01_10pto.raw	Raw
	2024MK013_SOBO_001to030_report.tsv	Tabular
	2024MK013_SOBO_002_01_10pto.raw	Raw
	2024MK013_SOBO_003_01_10pto.raw	Raw
	2024MK013_SOBO_004_01_10pto.raw	Raw

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The SR protein kinase Sky2 is involved in regulation of dipeptide transport in Candida albicans

Project description:Metabolic adaption to different host niches is one of the most important virulence traits of human fungal pathogens. The metabolic versatility of fungi and other cellular processes such as proliferation, morphogenesis and stress responses are tightly regulated by complex networks in which protein kinases play a crucial role. Serine-arginine (SR) protein kinases are highly conserved in all eukaryotes, but their function in pathogenic Candida spp. has not yet been investigated. C. albicans genome encodes two (Sky1, Sky2) and Candida glabrata one (Sky1) homolog of the human SR protein kinase 1 (SRPK1). We utilized deletion strains of the respective genes in both fungi in order to examine their cellular functions. C. glabrata and C. albicans strains lacking SKY1 exhibited higher resistance to osmotic stress and toxic polyamine concentrations to their ortholog in the model yeast Saccharomyces cerevisiae Sky1. Deletion of SKY2 in C. albicans resulted in impaired utilization of dipeptides as the sole nitrogen source. Subsequent phosphoproteomic analysis identified Ptr22, a transporter of di- and tri-peptides in C. albicans, as a potential Sky2 substrate. Overexpression of PTR22 in the sky2∆ restored the ability to grow on dipeptides as the sole nitrogen source and rendered the cells more susceptible to the dipeptide antibiotics Polyoxin D and Nikkomycin Z. Altogether, our results demonstrate that the two SR-like protein kinases in C. albicans have divergent functions: C. albicans and C. glabrata Sky1 is functionally similar to Sky1 in S. cerevisiae, whereas Sky2 regulates uptake of dipeptides.

2022-05-09 | PXD027612 | Pride

Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics

Project description:Mass spectrometry-based proteomics has advanced with the integration of experimental and predicted spectral libraries, which have significantly improved peptide identification in complex search spaces. However, challenges persist in distinguishing some peptides with close retention times and nearly identical fragmentation patterns. In this study, we conducted a theoretical assessment to quantify the prevalence of indistinguishable peptides within the human canonical proteome and immunopeptidome using state-of-the-art retention time and spectrum prediction models. By quantifying the proportion of peptides posing challenges to unequivocal identification, we set the accessible portion within a given proteome, thus establishing the current boundaries of the field, and underscore the effectiveness of contemporary analytical methodologies in resolving the complexity of the human proteome and immunopeptidome via mass spectrometry.

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Melanoma miRNA trafficking triggers the tumor primary niche formation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-08-09 | E-GEOD-72620 | biostudies-arrayexpress

Genome-wide gene expression analysis of HL60 cells and its alpha particle-resistant derivative RA11, gamma resistant-derivative RG8, and vincristine resistant-derivative RV+ at baseline and following 8Gy gamma IR and ~2Gy alpha IR

Project description:The purpose of this study was to identify genes that were differentially expressed in radiation-sensitive, naïve HL60 cells, and the derivatives created in our laboratory as indicated in the 'sample title'. We wanted to identify genes that were differentially expressed both before and after ionizing radiation (IR) exposure, from both a single dose of gamma rays and a single dose of alpha particles, at 4h following IR exposure. The data were used to identify genes that could be driving radioresistance in each respective cell line. The four cell lines, HL60, RA11, RG8, and RV+ were all analyzed at control (0Gy) radiation dose, 8Gy gamma rays, and ~2Gy alpha particles. Samples were collected from each cell line, for each dose, 4h following radiation exposure. The samples were collected from three independent experiments from three consecutive days in cell culture.

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Fkbp5 Gene Deletion: Impacts on Circadian Rhythmicity and Brain Proteomics in Aged Mice

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2024-09-05 | PXD049439 | Pride

Analysis for expression of genes in multiple myeloma cells treated with PRIMA-1Met or dimethyl sulfoxide (DMSO) control

Project description:Targeting p53 by the small molecule PRIMA-1Met/APR-246 has shown promising preclinical activity in various cancer types. However, the mechanism of PRIMA-1Met-induced apoptosis is not completely understood and its effect on multiple myeloma (MM) cells is unknown. In this study we evaluated anti-tumor effect of PRIMA-1Met alone or combined with current anti-myeloma agents in MM cell lines, patient samples, and a mouse xenograft model. Results of our study showed that PRIMA-1Met decreased the viability of MM cells irrespective of p53 status with limited cytotoxicity toward normal hematopoietic cells. PRIMA-1Met restored wild type conformation of mutant p53 and induced activation of p73 up-regulating Noxa and down-regulating Mcl-1 without significant modulation of p53 level. Importantly, PRIMA-1Met delayed tumor growth and prolonged survival of mice bearing MM tumor. To identify the potential targets of PRIMA-1Met, we performed gene expression profiling (GEP) by microarray in three different cell lines harboring wild type, mutant or null p53 and analysed differential expression of target genes between PRIMA-1Met treated and non-treated samples. Based on our we conclude that treatment of MM cells with PRIMA-1Met lead to induction of p73-mediated apoptosis by up-regulating Noxa and down-regulating Mcl-1 irrespective of p53 status. MM.1S, U266, and 8266R5 cells were treated with 20, 40, and 40 ÂµM PRIMA-1Met, respectively for 8 hrs and total RNA was isolated. Gene expression was analyzed with Illumina RNA analysis Beadchips (Illumina Inc. San Diego, CA) representing 48,000 human genes (Human HT12). Array data analysis was carried out with Bead Studio software. Genes showing at least a 2.0-fold difference in expression levels between control and PRIMA-1Met-treated cells were considered to be modulated by PRIMA-1Met.

2013-05-04 | E-GEOD-46609 | biostudies-arrayexpress

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Project description:Structural and functional changes of the choroid plexus (ChP) have been reported in Alzheimer’s disease (AD). Nonetheless, the role of the ChP in the pathogenesis of AD remains largely unknown. We aim to unravel the relation between ChP functioning and core AD pathogenesis using a unique proteomic approach in mice and humans. We used an APP knock-in mouse model, APPNL-G-F, exhibiting amyloid pathology, to study the association between AD brain pathology and protein changes in mouse ChP tissue and CSF using liquid chromatography mass spectrometry. Mouse proteomes were investigated at the age of 7 weeks (n=5) and 40 weeks (n=5). Results were compared with existing human AD CSF proteomic data (n=496) to identify key proteins and pathways associated with ChP changes in AD.

2024-08-10 | PXD052590 | Pride

Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma (DDLS) part 1

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2013-09-24 | E-GEOD-50749 | biostudies-arrayexpress

microRNA-like off-target transcript regulation by siRNAs

Project description:siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models. Hepa1-6 mouse hepatoma cell line and HUH7 and PLC/PRF/5 human hepatoma cell lines were transfected in 6-well plates using Lipofectamine RNAiMAX and siRNA duplexes at a final concentration of 10 nM. For in vitro analysis, RNA was extracted at 6, 12, 24, and 48 h post-transfection. For in vivo studies, mouse livers were harvested 3 d following a single administration of APOB siRNA (3 mg/kg) formulated in lipid nanoparticles. For details, please see: J. Burchard, A.L. Jackson, V. Malkov, R.H.V. Needham, Y. Tan, S.R. Bartz, H. Dai, A.B. Sachs and P.S. Linsley. microRNA-like off-target transcript regulation by siRNAs is species specific. RNA 15 (2009)

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