A549 cell line gene expression profiling in response to HBCD
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Tim Williams
PROVIDER: E-MTAB-2174 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Influenza A Virus (IAV) is a recurring respiratory virus with antiviral therapies of limited use. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry (AP-MS) and global phosphoproteomic and protein abundance analyses with three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we mapped 332 IAV-human protein-protein interactions (PPIs) and identified 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza revealed several genes, including the structural scaffold protein AHNAK, with predicted loss-of-function variants that were also identified in our proteomic analyses. Of our identified host factors, 54 significantly altered IAV infection upon siRNA knockdown, and two factors, COPB1 and AHNAK, were also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppressed IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT. This project includes endogenous IP data from A549 cells and NHBE cells infected with H5N1 IAV validating IAV-host PPIs M2-ATP6V1A and NEP-AHNAK, respectively. M2-ATP6V1A and NEP-AHNAK PPIs were first identified in AP-MS data that is submitted under its own dataset identifier (PXD036077).
2023-07-25 | PXD041663 | Pride
Project description:The human lung cancer cell line A549 was cultured in media alone, with cyclophosphamide (CPM), oxaliplatin (OXP) or DMSO alone for 72 hours. The exhausted culture media were aspirated and stored at -20C. Peripheral blood mononuclear cells (PBMCs) were isolated from four pathologically healthy donor buffy coats using Histopaque-1077. Following removal of red blood cell and platelet contamination, monocytes were isolated using magnetic beads coated with anti-CD14. Cells were resuspended and cultured in a DC-maturing medium for 7 days. Non- and loosely-adherent cells (the DC fraction) were harvested and purity assessed by CD11c/HLA-DR/CD14 immuno-discrimination by flow cytometry. 1x10^5 unstimulated DCs were cultured with tumour derived supernatants or culture media alone for 24 hours. DCs were then harvested and RNA isolated by Trizol. Total RNA was labelled and hybridised to Illumina Human HT-12v3 arrays. A separate aliquot of DCs from each patient was exposed to supernatant derived from tumour treated with OXP; changes in CD80, CD83 and CD86 were measured and DC populations showing a greater than two-fold up-regulation of these markers were classified as "GOOD_DC".
2011-04-01 | E-MTAB-389 | biostudies-arrayexpress
Project description:Background & Aims Patient-derived gastrointestinal organoids are powerful tools for studying human physiology and disease. However, generating organoids requires prompt isolation and culture of fresh tissue, which is labor and time intensive, placing restraints on basic and clinical research. For example organoid biobanking efforts, or the ability to obtain specimens from distant locations that lack the expertise to culture organoids, is limited by current approaches. We sought to develop a method by which tissue biopsies from patients could be cryo-preserved, stored, or shipped, and later thawed in order to establish live organoid cultures. Methods A method for freezing and recovery, along with straightforward isolation methods using readily available materials were developed. Epithelial isolation and culture conditions were optimized to promote cell survival and the establishment of long-term culture post-thawing. Results Patient biopsies from stomach, duodenum, ileum, colon and from adenomateous colonic polyps were frozen, subsequently thawed and used to successfully establish patient-specific epithelium-only organoid cultures with 100% efficiency (n=31 independent patient biopsies from different regions of the GI tract). Frozen tissue could be shipped internationally and across the United States and used to establish successful organoid cultures. Organoid cultures could be expanded, passaged and frozen down for long-term storage. RNA-sequencing demonstrates that organoids derived from fresh tissue or from frozen biopsies are >99% transcriptionally identical. Conclusions Cryo-preservation of human tissue biopsies followed by the establishment of long-term, expandable cultures has negligible effect on transcription when compared to freshly prepared organoids, and will be of immense benefit to research and for clinical applications. This technique will allow for the establishment of biobanks of human tissues that can be revived and cultured in the future as well as transported across the globe for research, therapeutic or diagnostic use in remote labs and/or clinics.
2018-06-30 | E-MTAB-6516 | biostudies-arrayexpress
Project description:Identification of differentially expressed genes in HUVEC senescence and tBHP treatment.
2010-07-30 | E-MEXP-2283 | biostudies-arrayexpress
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Project description:Infection with the parasite Toxoplasma gondii leads to production of interferon gamma (IFN) that stimulates cells to upregulate defence proteins targeting the parasite for cell intrinsic elimination or growth restriction. Various host defence mechanisms operate at the parasitophorous vacuole (PV) in different human cell types leading to PV disruption, acidification, or membrane envelopment. Ubiquitin and p62 are players in all human host control mechanisms of Toxoplasma, but other unifying proteins have not been identified. Here, we show that p97/valosin-containing protein (VCP), as well as its associated proteins ANKRD13A and UBXD1 control Toxoplasma infection while recruited to the PV in IFN-stimulated endothelial cells. Convergent deposition of ANKRD13A, p97/VCP and UBXD1 onto the same vacuole is dependent on vacuolar ubiquitination and observed within 2h post-infection. ANKRD13A, p97/VCP and UBXD1 all drive the acidification mechanism of the vacuole, which is the IFN-dependent control pathway of Toxoplasma in endothelial cells. We assessed p97/VCP in Toxoplasma control in various human cells and demonstrate that p97/VCP is a universal IFN-dependent host restriction factor targeting the Toxoplasma PV in epithelial (HeLa) and endothelial cells (HUVEC), fibroblasts (HFF) and macrophages (THP1).
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Project description:Prolonged use of glucocorticoids can lead to the formation of a cataract, however the mechanism is not known. We recently reported the presence of the functional glucocorticoid receptor in immortalized cultured mammalian lens epithelial cells (Gupta & Wagner, Invest Ophthalmol Vis Sci 2003), but the short term biological effect of glucocorticoid action in lens epithelial cells is not known. This study seeks to examine glucocorticoid induced changes in global gene expression in LECs. RNA isolated from HLE B-3 cells, treated with Dex or Veh for 4 or 16 hours, was used to analyze global changes in gene expression by microarray hybridization. Microarray studies at 2 time periods demonstrate that glucocorticoids modulate gene expression in immortalized human LECs, reveal novel changes in gene expression, and confirms an endogenous genomic lens glucocorticoid response. Experiment Overall Design: HLE B-3 cells were treated with 1uM dexamethasone or vehicle for 4 or 16 hours in triplicate. Total RNA was converted to cRNA and hybridized to Affymetrix HUM_133A genechips. Images were acquired using the Affymetrix GeneArray scanner. Data was extracted using Affymetrix Microarray Suite 5.0.
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
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