Genomic and transcriptomic profiling of signalling networks in follicular lymphoma
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ABSTRACT:
PROVIDER: EGAS00001002175 | EGA |
REPOSITORIES: EGA
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Project description:Data Access Committee EGAC00001000577
| EGAC00001000577 | EGA
Project description:The development of affinity purification technologies together with mass spectrometric analyses of the purified protein mixtures (AP-MS) has been used both to identify new protein-protein interactions and to define the subunit composition of protein complexes. Transcription factor protein interactions, however, have not been systematically analyzed using these approaches. Here, we have investigated whether ectopic expression of an affinity tagged transcription factor as bait in AP-MS experiments perturbs gene expression in cells resulting in false positive identification of bait associated proteins when typical experimental controls are used. Using quantitative proteomics and RNA-Seq, we determined that the increase in the abundance of a set of proteins caused by overexpression of the transcription factor RelA is not sufficient for these proteins to then copurify non-specifically and be misidentified as bait associated proteins. Therefore typical controls should be sufficient and a number of different baits can be compared with a common set of controls. This is of practical interest when identifying bait interactors from a large number of different baits. As expected, we found several known RelA interactors enriched in our RelA purifications (NFêB1, NFêB2, Rel, RelB, IêBá, IêBâ and IêBå). We also found several proteins not previously described in association with RelA, including the small mitochondrial chaperone Tim13. Using a variety of biochemical approaches, we further investigated the nature of the association between Tim13 and NFêB family transcription factors. The work here therefore provides a conceptual and experimental framework for analyzing transcription faction protein interactions. Gene expression profiles were assayed in triplicate from HEK293 cells expressing either Halo-RelA, Halo-NFkB1, or Halo tag alone.
2014-04-24 | E-GEOD-57027 | biostudies-arrayexpress
Project description:Inhaled polymyxins are increasingly used to treat pulmonary infections caused by multidrug-resistant Gram-negative pathogens. We have previously shown that apoptotic pathways, autophagy and oxidative stress are involved in polymyxin-induced toxicity in human lung epithelial cells. In the present study, we employed human lung epithelial cells A549 treated with polymyxin B as a model to elucidate the complex interplay of multiple signalling networks underpinning cellular responses to polymyxin toxicity. Polymyxin B induced toxicity (1.0 mM, 24 h) in A549 cells was assessed by flow cytometry and transcriptomics was performed using microarray. Polymyxin B induced cell death was 19.0 ± 4.2% at 24 h. Differentially expressed genes (DEGs) between the control and polymyxin B treated cells were identified with Student's t-test. Pathway analysis was conducted with KEGG and Reactome and key hub genes related to polymyxin B induced toxicity were examined using the STRING database. In total we identified 899 DEGs (FDR < 0.01), KEGG and Reactome pathway analyses revealed significantly up-regulated genes related to cell cycle, DNA repair and DNA replication. NF-κB and nucleotide-binding oligomerization domain-like receptor (NOD) signalling pathways were identified as markedly down-regulated genes. Network analysis revealed the top 5 hub genes (i.e., degree) affected by polymyxin B treatment were PLK1(48), CDK20 (46), CCNA2 (42), BUB1 (40) and BUB1B (37). Overall, perturbations of cell cycle, DNA damage and pro-inflammatory NF-κB and NOD-like receptor signalling pathways play key roles in polymyxin-induced toxicity in human lung epithelial cells. Noting that NOD-like receptor signalling represents a group of key sensors for microorganisms and damage in the lung, understanding the mechanism of polymyxin-induced pulmonary toxicity will facilitate the optimisation of polymyxin inhalation therapy in patients.
| S-EPMC8944768 | biostudies-literature
Project description:Most flowering plants must defend themselves against herbivores for survival and attract pollinators for reproduction. Although traits involved in plant defence and pollinator attraction are often localised in leaves and flowers, respectively, they will show a diffuse evolution if they share the same molecular machinery and regulatory networks. We performed RNA-sequencing to characterise and compare transcriptomic changes involved in herbivory-induced defences and flower development, in tomato leaves and flowers, respectively. We found that both the herbivory-induced responses and flower development involved alterations in jasmonic acid signalling, suppression of primary metabolism and reprogramming of secondary metabolism. We identified 411 genes that were involved in both processes, a number significantly higher than expected by chance. Genetic manipulation of key regulators of induced defences also led to the expression changes in the same genes in both leaves and flowers. Targeted metabolomic analysis showed that among closely related tomato species, jasmonic acid and α-tomatine are correlated in flower buds and herbivory-induced leaves. These findings suggest that herbivory-induced responses and flower development share a common molecular machinery and likely have coevolved in nature.
| S-EPMC8493932 | biostudies-literature
Project description:The development of affinity purification technologies together with mass spectrometric analyses of the purified protein mixtures (AP-MS) has been used both to identify new protein-protein interactions and to define the subunit composition of protein complexes. Transcription factor protein interactions, however, have not been systematically analyzed using these approaches. Here, we have investigated whether ectopic expression of an affinity tagged transcription factor as bait in AP-MS experiments perturbs gene expression in cells resulting in false positive identification of bait associated proteins when typical experimental controls are used. Using quantitative proteomics and RNA-Seq, we determined that the increase in the abundance of a set of proteins caused by overexpression of the transcription factor RelA is not sufficient for these proteins to then copurify non-specifically and be misidentified as bait associated proteins. Therefore typical controls should be sufficient and a number of different baits can be compared with a common set of controls. This is of practical interest when identifying bait interactors from a large number of different baits. As expected, we found several known RelA interactors enriched in our RelA purifications (NFêB1, NFêB2, Rel, RelB, IêBá, IêBâ and IêBå). We also found several proteins not previously described in association with RelA, including the small mitochondrial chaperone Tim13. Using a variety of biochemical approaches, we further investigated the nature of the association between Tim13 and NFêB family transcription factors. The work here therefore provides a conceptual and experimental framework for analyzing transcription faction protein interactions.
2014-04-24 | GSE57027 | GEO
Project description:Phenotypes representative of normal, transformed and experimentally manipulated human B cells related to the germinal center structure.
2005-04-04 | GSE2350 | GEO
Project description:Clonal variation, wherein a range of specific productivities of secreted proteins are observed from supposedly identical transformants, is an ingrained aspect of working with Pichia pastoris. It means that a significant number of transformants need to be tested to obtain a representative sample, and in commercial protein production, companies regularly screen thousands of transformants to select for the highest secretor. Here we have undertaken a detailed investigation of this phenomenon by characterising clones transformed with the human serum albumin gene. In order to evaluate the prevalence and underlying causes of clonal variation, nine strains were selected, each transformed with a single copy of the human serum albumin (HSA) gene. All strains were subjected to a wide-ranging evaluation to understand the implications of this phenomenon.
2017-05-26 | E-MTAB-5124 | biostudies-arrayexpress
Project description:Follicular lymphoma (FL) is the second most common B-cell malignancy representing one quarter of Non-Hodgkin's Lymphomas. Although the disease has a relatively long median survival, the illness follows a fluctuating course of progression punctuated by remissions of variable duration. For as many as half of patients, transformation to a more aggressive lymphoma (t-FL) may occur; this event is often associated with a particularly poor response to treatment. SNP analysis has revealed the presence of large regions of homozygosity in the absence of copy number change. These events can result in the selection of of daughter cells made homozygous for a pre-existing mutation. We have used SNPs array technology to investigate regions of loss of hetrozygosity in the absence of copy number change in order to establish the contribution of these abnormalities to the evolution of FL and t-FL. Experiment Overall Design: DNA from 26 pairs of follicular and transformed follicular lymphoma samples and 3 cell lines were analysed using Affymetrix 10K SNP arrays. The genotype data of transformed follicular lymphoma samples were compared with the data from the corresponding follicular lymphoma sample.
2008-06-17 | E-GEOD-7425 | biostudies-arrayexpress
Project description:Granulosa cells play important roles in ovarian follicular development. To better understand the molecular mechanisms involved in this physiological process in chicken, high-throughput transcriptome analyses were performed to study the expression profiles of granulosa cells harvested from 6 mm white follicles, F5 follicles and F1 follicles. The analyses elucidated a clear tendency of granulosa cells in shifting its expression profile from proliferation to differentiation during follicular development. Transcripts down-regulated during this process were mainly associated with cell division, cell cycle and DNA replication while the up-regulated transcripts were related to ribosomal function, lipid metabolism and protein synthesis. Our study for the first time provides the complete gene expression profiles along follicular development supporting the active involvement of many genes characterized in cell signaling (AMH, Inhibins, Activins, BMPs) and transcription factors (SMAD3, SMAD5, ID1, ID2, ID3). Their temporal expression profiles support the notion of continual cross-talk between granulosa cells and its neighboring cells and shed light on the mechanisms behind avian follicular selection and pave the way to the better understanding of reproductive efficiency.
| S-EPMC6445143 | biostudies-literature