RNA-seq of human neutrophil-like cell line PLB-985 at various stages of differentiation with CRISPR knock-outs of H1 linker histones
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 3000
ORGANISM(S): Homo sapiens
SUBMITTER: Robert Streeck
PROVIDER: E-MTAB-8459 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Interferon-gamma (IFN-gamma) is approved as a drug to treat chronic granulomatous disease and osteopetrosis and is also used in hyperimmunoglobulin E syndromes. These primary immunodeficiencies involve defects in neutrophils/polymorphonuclear cells. Neutrophils mature in the bone marrow and then enter the blood where they quickly undergo apoptotic cell death with a half-life of 5-10 hours. Therefore we reasoned that IFN-gamma might exert its effects on neutrophils via prolonged exposure to cells undergoing maturation toward a terminally differentiated state in the marrow rather than by its brief exposure to short-lived circulating cells. To explore this possibility we made use of PLB-985 cells which are a myeloblast-like myeloid cell line that can be differentiated into a mature, neutrophil-like state by treatment with various agents including DMSO. In initial studies we investigated transcription and protein expression in PLB-985 cells undergoing DMSO-mediated maturation in the presence or absence of IFN-gamma and identified several classes of immunity related genes that were differentially expressed in the presence of the drug and could potentially explain the immune supportive properties of IFN-gamma. Next we explored if the effect of IFN-gamma on expression of these genes is dependent on whether the cells are undergoing maturation; to do this we compared the effects of IFN-gamma on cells cultured with and without DMSO. For a subset of genes the expression level changes caused by IFN-gamma were much greater in maturing cells than non-maturing cells. These findings indicate that developmental changes associated with cell maturation can modulate the effects of IFN-gamma and supports our hypothesis that the effects of the drug on developing neutrophils in the bone marrow may be very different from its effects on mature cells in the blood. We also compared the effects on gene expression of applying IFN-gamma either during DMSO mediated PLB-985 cell maturation or after maturation i.e. IFN-gamma was applied to already mature cells. For some genes we found that IFN-gamma applied to mature cells caused large changes in expression similar to those seen when IFN-gamma was applied during maturation, however for other genes no effect was seen when drug was applied to mature cells but large effects were seen when drug was applied during DMSO treatment. This data suggests that, in the former class of genes, the effects of IFN-gamma application during maturation are largely the result of the effects of the drug on cells approaching full maturity but in the latter class of genes the effects of IFN-gamma only become apparent when it is present throughout maturation. This further supports our hypothesis that the effects of IFN-gamma are modulated by developmental changes associated with cell maturation.
2017-08-31 | E-MTAB-5690 | biostudies-arrayexpress
Project description:Fungal infections remain a tremendous source of global morbidity and mortality, with more than 1 billion individuals affected by fungal infections each year. Invasive infections are particularly dangerous and kill numbers on par with tuberculosis or malaria. Aspergillus fumigatus is a major source of invasive fungal infections in humans, and is particularly dangerous to the immunocompromised. In many cases, research into invasive fungal infections is limited by a lack of model systems. In this study we hypothesized that cultured, differentiated human PLB-985 neutrophil-like cells could serve as model system to study the host-pathogenesis of A. fumigatus. We tested this hypothesis by defining the phagocytosis and intracellular trafficking of A. fumigatus conidia by PLB-985 cells, the production of neutrophil extracellular traps, and by characterizing extracellular vesicles produced in response to infection. As part of this analysis, we performed a detailed LC-MS/MS-based proteomic comparison of extracellular vesicles isolated by two different methods, centrifugation-based isolation or size-exclusion chromatography. We find numerous similarities between primary neutrophils and PLB-985 cells that suggest differentiated PLB-985 cells can serve as a tractable in vitro model system for further study of many aspects of A. fumigatus pathogenesis.
2021-07-30 | PXD027032 | Pride
Project description:The relevance of mitochondrial proteostasis for the differentiation and function of hematopoietic and immune cells is unknown. Dissecting the HCLS1-associated protein X-1 (HAX1) –related protein network, we define a functional CLPB-HAX1-PRKD2-HSP27 axis with critical importance for the differentiation of neutrophil granulocytes and thus elucidate molecular mechanisms underlying congenital neutropenia in patients with mutations in HAX1 and CLPB. As shown by SILAC proteomics, CLPB and HAX1 control the balance of protein synthesis and persistence in mitochondria, leading to dysfunction of the respiratory complex 1. Impaired mitochondrial proteostasis is associated with decreased abundance of the serine-threonine kinase PRKD2 and Ser82-phosphorylated HSP27. Cellular defects in HAX1-/- cells can be functionally reconstituted by HSP27. Thus, mitochondrial proteostasis emerges as a critical mechanism governing the differentiation and function of neutrophil granulocytes.
2022-05-19 | PXD023790 | Pride
Project description:Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1.4 (sh120) or multiple H1 variants (sh225), or overexpressing WT or K26A mutant HA-tagged H1.4. T47D-MTVL, breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter, is stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA. Stable breast cancer-derived cell lines expressing an shRNA against one of each of the histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox, in duplicate, and RNA extracted for microarray hybridization. Cell lines used: inducible shRNA against H1.4 or multiple H1 variants, and random shRNA-expression vector. Stable breast cancer-derived cell lines expressing the histone H1.4 isoform, WT or K26A, HA-tagged, in duplicate, and RNA extracted for microarray hybridization. Cell lines used: overexpressing H1.4 WT or K26A mutant.
2014-05-16 | E-GEOD-55786 | biostudies-arrayexpress
Project description:Genome wide chromatin profile for Histone H1.4 (pan-H1.4) and Phosphorylated H1.4 (pS187-H1.4)
| PRJNA566437 | ENA
Project description:Lambda interferons IFNL1-3 mediate antiviral immunity by inducing interferon sensitive genes (ISGs) in epithelial tissues. Contrarily, a variant creating the functional gene IFNL4 is associated with impaired clearance of hepatitis C virus (HCV) despite of higher liver expression of ISGs in untreated HCV patients. We aimed to explore IFNL4 signaling mechanism by comparing expression profiles from human hepatic cell line clones with genetic modifications influencing the ISG signaling pathway (IFNLR1/IL10R2 knockouts, IFNL4/IFNL3 expression stimulation by transfection).
2021-12-31 | E-MTAB-8916 | biostudies-arrayexpress
Project description:In this study, we used a quantitative redox proteomic method (OxICAT) to assess the in vivo thiol oxidation status of phagocytized E. coli. The majority (65.5%) of identified proteins harbored thiols that were significantly oxidized (>30%) upon phagocytosis. A substantial number of these proteins are from major metabolic pathways or are involved in cell detoxification and stress response, suggesting a systemic breakdown of the bacterial cysteine proteome in phagocytized bacteria.
2019-01-07 | PXD011386 | Pride
Project description:Rahman syndrome (RMNS) is a rare genetic disorder characterized by mild to severe intellectual disability, hypotonia, anxiety, autism spectrum disorder, vision problems, bone abnormalities, and dysmorphic facies. De novo heterozygous mutations in H1-4 encoding the linker histone H1.4 are found in individuals with RMNS; however, the underlying mechanisms causing significantly impaired neurodevelopment are not understood. So far, all neurodevelopmental associated mutations in H1-4 are small insertions or deletions that create a shared frameshift, resulting in a H1.4 protein that is both truncated and possessing an abnormal C-terminus frameshifted tail (H1.4 CFT). To expand understanding of mutations and phenotypes associated with mutant H1-4, we identified additional and new DNA variants at both the C- and N-terminus of H1.4. The clinical features of mutations identified at the C-terminus are consistent with other reports that strengthen the support of pathogenicity of H1.4 CFT. However, the pathogenicity of disrupting variants at the N-terminus could not be determined. To understand how H1.4 CFT may disrupt brain function, we exogenously expressed wildtype or H1.4 CFT protein in primary rat hippocampal neurons and assessed neuronal structure and function. Genome-wide transcriptome analysis revealed ~400 genes altered specifically in the presence of H1.4 CFT. Neuronal genes downregulated by H1.4 CFT were enriched for functional categories involved in synaptic communication and neuropeptide signaling. Neurons expressing H1.4 CFT showed reduced activity on extracellular electrode arrays, indicating that these transcriptional changes were sufficient to disrupt physiological neuronal function. These data are the first to characterize the consequence of H1.4 CFT in neurons. Our data provide initial insights into causes of neurodevelopmental impairments associated with these frameshift mutations in the C-terminus of H1.4 and highlight the need for future studies on the function of normal histone H1.4 in neurons.
2021-07-26 | GSE180609 | GEO
Project description:In this study, we use novel, highly specific custom antibodies against a linker histone variant and its modified form to conduct chromatin immunoprecipitation (ChIP) followed by Next Generation Sequencing (NGS) to investigate their binding profiles as a result of transcription inititation. Here we use an estrogen responsive breast cancer cell line, MCF7 to study the enrichment patterns of Histone H1.4 (pan-H1.4) and Phosphorylated H1.4 (pS187-H1.4) across the genome as a result of a short estrogen treatment (30 mins). We find that pS187-H1.4 is preferentially enriched at the promoters of active genes as opposed to the depletion of pan-H1.4 at the same site. Additionally, we use a short treatment of Flavopiridol- an inhibitory drug specific for Cyclin-dependent Kinase-9 (CDK9) which is responsible for the phosphorylation of H1.4 cells, to demonstrate the quenching of this signal at sites specificially activated as a result of the estrogen treatment. This demonstrates for the first time that pS187-H1.4 is associated with active genes and may even be involved in the regulation of gene activity.
2020-09-01 | GSE137748 | GEO
Project description:Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1.4 (sh120) or multiple H1 variants (sh225), or overexpressing WT or K26A mutant HA-tagged H1.4.
2014-05-16 | GSE55786 | GEO