Disclosing potential therapeutic targets associated with Osimertinib resistance in non-small cell lung cancer cell line H1975
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo Sapiens
SUBMITTER: 
Xuexia Tong
PROVIDER: PXD043855 | iProX | Tue Jul 18 00:00:00 BST 2023
REPOSITORIES: iProX
Similar Datasets
Project description:Osimertinib, a third-generation epidermal growth factor receptor tyrosine kinase inhibitor, is a highly effective and valuable treatment option for advanced non-small cell lung cancer (NSCLC) patients with EGFR mutations, like T790M. However, acquired resistance ultimately limits its clinical application. In this study, we constructed H1975/OSI cell lines and utilized potentially complementary transcriptomic and proteomic techniques, which may provide insight into the intricately complex molecular mechanisms, to reveal potential therapeutic targets associated with Osimertinib resistance. Uni-omics and multi-omics analyses were conducted on the transcriptomic and proteomic (4D label-free) expression profiles, which involved differential expression analysis, GO functional annotation and KEGG pathway enrichment analysis, correlation analysis of transcription factors, PPI network and Cytoscape analysis. We highlighted multiple signaling pathways and eleven hub-genes, including NOP56, DDX21, PDCD11, CCNB1, TOP21, KPNA2, DDX5, EFTUD2, BRCA1, LMNB1 and HIF1A, that may be the key to overcoming resistance. Further validation of these targets and molecules in preclinical and clinical studies could lead to the development of new and more effective treatment options for H1975-resistant patients.
2024-08-05 | GSE236654 | GEO
Project description:Fresh MEC1 cells (chronic lymphocytic leukemia) (ACC-497, DSMZ) previously untreated and treated in cultures in vitro with glycodendrimers (nanoparticle with maltotriose on the surface). MEC1 cells were centrifuged after incubation with drugs or dendrimers. Agilent’s Low Input Quick Amp Labeling Kit was used to generate fluorescent cRNA (complimentary RNA) with a sample input 100ng of total RNA for two-color processing. The method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP. Amplification is typically at least a 100-fold from total RNA to cRNA with the use of this kit. cRNA quantification had been done using NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1. Arrays were placed onto the gaskets and than to the slide chamber in rotisserie in a hybridization oven set. Hybrydization was carried out at 65-Celsius degrees for 17 hours. Arrays were scanning using Agilent Scanner. Scan resolution was set up for 3μM. Microarray gene expression profiling. Intensity of gene expression in MEC1 cells before treatment was compared with the gene expression signals in MEC1 cells from the same cell culture after 4 and 48 hours of treatment. MEC1 cells were treated with PPI-G4-OS-Mal-III dendrimer, PPI-G4-DS-Mal-III, Fludarabina. Sample titles represent; A = Cy3 B = Cy5 R = reference (48h incubation) R4 = reference (4h incubation) 1 = PPI-G4-DS-Mal III (1st cell culture flask) (48h incubation) 2 = PPI-G4-DS-Mal III (2nd cell culture flask)(48h incubation) 3 = PPI-G4-OS-Mal III (1st cell culture flask)(48h incubation) 4 = PPI-G4-OS-Mal III (2nd cell culture flask)(48h incubation) 5 = PPI-G4-DS-Mal III (4h incubation) 6 = PPI-G4-OS-Mal III (4h incubation) 7 = FA (4h incubation) 8 = FA (48h incubation)
2015-04-22 | E-GEOD-68094 | biostudies-arrayexpress
Project description:<h4><strong>OBJECTIVE:</strong> Emerging evidence suggests that glucose depletion (GD)-induced cell death depends on system Xc-, a glutamate/cystine antiporter extensively studied in ferroptosis. However, the underlying mechanism remains debated. Our study confirmed the correlation between system Xc- and GD-induced cell death and provided a strategic treatment for oral squamous cell carcinoma (OSCC).</h4><p><strong>METHODS:</strong> qPCR and Western blotting were performed to detect changes in xCT and CD98 expression after glucose withdrawal. Then, the cell viability of OSCCs under the indicated conditions was measured. To identify the GD-responsible transcriptional factors of SLC7A11, we performed a luciferase reporter assay and a ChIP assay. Further, metabolomics was conducted to identify changes in metabolites. Finally, mitochondrial function and ATP production were evaluated using the seahorse assay, and NADP+/NADPH dynamics were measured using a NADP+/NADPH kit.</p><p><strong>RESULTS:</strong> In OSCCs, system Xc- promoted GD-induced cell death by increasing glutamate consumption, which promoted NADPH exhaustion and TCA blockade. Moreover, GD-induced xCT upregulation was governed by the p-eIF2α/ATF4 axis.</p><h4><strong>CONCLUSIONS:</strong> System Xc- overexpression compromised the metabolic flexibility of OSCC under GD conditions, and thus, glucose starvation therapy is effective for killing OSCC cells.</h4>
2024-01-16 | MTBLS5358 | MetaboLights
Project description:"The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations. STATegra methods address many aspects of the omics data integration problem such as the design of multiomics experiments, integrative transcriptional and regulatory networks, integrative variable selection, data fusion, integration of public domain data, and integrative pathway analysis. To support method development STATegra uses a model biological system, namely the differentiation process of mouse pre-B-cells. The STATegra consortium generated data focused on a critical step in the differentiation of B lymphocytes, which are key components of the adaptive immune system. Transcription factors of the Ikaros family are central to the normal differentiation of B cell progenitors and their expression increases in response to developmental stage-specific signals to terminate the proliferation of B cell progenitors and to initiate their differentiation. In particular, a novel biological system that models the transition from the pre-BI stage to the pre-BII subsequent stage, where B cell progenitors undergo growth arrest and differentiation, was used. The approach involves a pre-B cell line, B3 , and an inducible version of the Ikaros transcription factor, Ikaros-ERt2. Ikaros factors act to down-regulate genes that drive proliferation and to simultaneously up-regulate the expression of genes that promote the differentiation of B cell progenitors. Hence, in the B3 system, before induction of Ikaros, cells proliferate and their gene expression pattern is similar to proliferating B cell progenitors in vivo. Following Ikaros induction, B3 cells undergo gene expression changes that resemble those that occur in vivo during the transition from cycling to resting pre-B cells, followed by a marked reduction in cellular proliferation and by G1 arrest. On this system the consortium has created a high-quality data collection consisting of a replicated time course using seven different omics platforms: RNA-seq, miRNA-seq, ChIP-seq, DNase-seq, Methyl-seq, proteomics and metabolomics, which is used to assess and to validate STATegra methods."
2019-03-05 | PXD003263 | Pride
Project description:Primary outcome(s): 1. Evaluation of genome abnormality and gene expression by omics analysis of tumor etc. 2. TCR repertoire analysis and RNA expression analysis etc. of T cells in tumor tissue and peripheral blood. 3. Prediction and identification of tumor neo-antigen and evaluation of immunogenicity etc. 4. Analyze ctDNA(16S rRNA PCR) and feces of patients with advanced solid malignancies over time to profile and monitor cancer-related genomic alterations 5. Assessment of the relationship between the analysis above and clinical pathological features or therapeutic efficacy etc.
| 2648665 | ecrin-mdr-crc
Project description:The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of 'omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations. STATegra methods address many aspects of the 'omics data integration problem such as the design of multi-omics experiments, integrative transcriptional and regulatory networks, integrative variable selection, data fusion, integration of public domain data, and integrative pathway analysis. To support method development STATegra uses a model biological system, namely the differentiation process of mouse pre-B-cells. The STATegra consortium generated data focused on a critical step in the differentiation of B lymphocytes, which are key components of the adaptive immune system. Transcription factors of the Ikaros family are central to the normal differentiation of B cell progenitors and their expression increases in response to developmental stage-specific signals to terminate the proliferation of B cell progenitors and to initiate their differentiation. In particular, a novel biological system that models the transition from the pre-BI stage to the pre-BII subsequent stage, where B cell progenitors undergo growth arrest and differentiation, was used. The approach involves a pre-B cell line, B3, and an inducible version of the Ikaros transcription factor, Ikaros-ERt2. Ikaros factors act to down-regulate genes that drive proliferation and to simultaneously up-regulate the expression of genes that promote the differentiation of B cell progenitors. Hence, in the B3 system, before induction of Ikaros, cells proliferate and their gene expression pattern is similar to proliferating B cell progenitors in vivo. Following Ikaros induction, B3 cells undergo gene expression changes that resemble those that occur in vivo during the transition from cycling to resting pre-B cells, followed by a marked reduction in cellular proliferation and by G1 arrest. On this system the consortium has created a high-quality data collection consisting of a replicated time course using seven different 'omics platforms: RNA-seq, miRNA-seq, ChIP-seq, DNase-seq, Methyl-seq, proteomics and metabolomics, which is used to assess and to validate STATegra methods. The STATegra experimental design consists of a 6 point time course that captures the differentiation of B3 cells containing Ikaros-ERt2 upon Ikaros induction within a 24 hr period. The process was sampled at 0, 2, 6, 12, 18, and 24 hrs respectively after Ikaros induction by Tamoxifen. As control, B3 cells transfected with an empty vector were treated and sampled in the same way as the inducible line. Eight different 'omic technologies were measured on this system: RNA-seq, miRNA-seq, DNase-seq, RRBS-seq, ChIP-seq, scRNA-seq, Proteomics and Metabolomics. Generally, three biological replicates were obtained per platform and were processed as independent batches. Metabolomics analysis was performed using 4 biological batches (7, 8, 9 and 10) and at times 0, 2, 6, 12, 18 and 24 hrs respectively. Each sample was analyzed using gas chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS).
2016-12-15 | MTBLS283 | MetaboLights
Project description:Permanent fish cell lines offer promising alternatives to traditional animal models for environmental risk assessment of chemicals. However, to facilitate broader uptake into toxicity testing practice, a better understanding of functional capacities and expression of toxicologically relevant molecular targets is needed. Here, we present an extensive molecular profiling of the zebrafish embryonic cell line PAC2, combining global proteomics across cell population growth phases (over 7300 protein groups) with matched transcriptomics at exponential and stationary phases (over 14500 transcripts). Proteome coverage was sufficiently deep to reveal functional insights consistent with those derived from transcriptomics data, despite differences in the total number of measured genes. Major gene expression shifts detected upon transition from exponential to stationary cell population growth phase indicated reduction in DNA replication, translation, metabolism, and cell cycle regulation, along with increased stress and immune system responses, and extracellular matrix remodeling. Functional annotation revealed expression of core cellular processes along with a number of toxicologically relevant pathways, including xenobiotic metabolism, stress signaling, and nuclear receptors responsive to important chemical classes, such as steroids (e.g., estrogens, glucocorticoids) and chemicals known to disrupt lipid metabolism, such as through interaction with peroxisome proliferation activating receptors. These findings reinforce the potential of PAC2 cells to offer a versatile in vitro model for studying fish cell biology and omics-enhanced exploration of chemical toxicity mechanisms, aided by the well-developed molecular annotation in zebrafish. Moreover, the analysis approaches developed in this work offer a blueprint for molecular baseline characterization of other fish cell lines. This work thus strengthens the mechanistic foundation supporting the use of fish cell lines as alternative models in aquatic toxicity testing and risk assessment.
2025-12-05 | PXD066565 | Pride
Project description:SCL/TAL1, a tissue-specific transcription factor of the basic helix-loop-helix (bHLH) family, and c-Kit, a tyrosine kinase receptor, control hematopoietic stem cell survival and quiescence. Here we report that SCL and c-Kit signaling control a common gene expression signature, of which 19 genes are associated with apoptosis. In vivo, SCL levels are limiting for the clonal expansion of Kit+ multipotent and erythroid progenitors. In addition, increased SCL expression specifically enhances the sensitivity of multipotent and megakaryocyte/erythroid progenitors to Steel factor (KIT ligand), whilst a DNA binding mutant antagonizes KIT function and induces apoptosis in progenitors. We conclude that Scl operates downstream of Kit to support the survival of megakaryocyte/erythroid progenitors. Finally, higher SCL expression upregulates Kit in normal bone marrow cells and increases chimerism after bone marrow transplantation, indicating that Scl is also upstream of Kit. We conclude that Scl and Kit establish a positive feedback loop in multipotent and megakaryocyte/erythroid progenitors.
2013-07-06 | GSE48557 | GEO
Project description:All cell lines were cultured according to the specifications outlined by ATCC. Cell lines were grown to 80% confluence, then serum-deprived in 0.5% FBS for 24 hours before harvesting. Cells were washed twice with Hank's Balanced Salt Solution (Invitrogen, Carlsbad, California) and drained. 1 mL of SDS extraction buffer (0.1M NaCl, 20 mM Trizma base, 25 mM EDTA, 0.5% w/v SDS) was added directly to the plate to lyse the cells. Cellular lysate was scraped off the plates, pipetted into a cryovial, and stored at 80C until DNA extraction. Lysates were treated with 200 ug/ml ProteinaseK at 50C overnight. DNA was precipitated with one volume of Isopropanol and dissolved in TE4 buffer. Cell lines were lysed in Phenol followed by a Phenol/Chloroform extraction. The aqueous layer was added to 70% ethanol and further purified by loading the RNA/Ethanol mix into an RNeasy Mini kit (Qiagen) column. Purification was continued and finalized as described in the RNeasy kit (Qiagen) Manual. We measured transcript levels in the 27 primary ovarian tumors and 15 cell lines using the HEEBO [16] oligonucleotide microarrays, containing 44,544 70-mer probes and printed at the Stanford Functional Genomics Facility. Detailed information on the HEEBO arrays is available at the Stanford Functional Genomics Facility website. Experimental methods. Microarray experiments were performed as described at the Brown lab website. Briefly, 500 ug of total RNA from each of the ovarian tumors were amplified using Amino Allyl Message Amp II aRNA Kit (Ambion, Austin, TX, USA). The aRNAs were labeled with Cy5 and co-hybridized with Cy3 labeled Stratagene reference aRNA. For some samples, the mRNA was amplified and hybridized in duplicate or triplicate. The samples were then hybridized to HEEBO microarrays. The arrays were scanned in a low-ozone environment using a GenePix 4000A microarray scanner and images were analyzed with Genepix 5.0 (Axon instruments, Union City, CA).
2011-02-12 | GSE27225 | GEO
Project description:This submission is a dataset of single-nucleus multi-omics of uninjured and injured spinal cords of mice harvested and profiled using 10x Multiome ATAC + Gene Expression kit.
2024-04-30 | GSE230765 | GEO