Effect of pharmacologic inhibition of KPNB1 by Importazole on gene expression of NB-4 cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1164748 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30787245_1.fastq.gz | Fastqsanger.gz | |||
| SRR30787245_2.fastq.gz | Fastqsanger.gz | |||
| SRR30787246_1.fastq.gz | Fastqsanger.gz | |||
| SRR30787246_2.fastq.gz | Fastqsanger.gz | |||
| SRR30787247_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Acute myeloid leukemia (AML) is the most common malignancy of the hematologic system with refractory relapse and limited treatments. Nucleocytoplasmic trafficking of biomolecules mediated by Karyopherin proteins plays vital roles in AML promotion and development, but the underlying mechanism is not clearly elucidated. KPNB1, a key member of Karyopherin beta subunits, is highly expressed in multiple cancers. Here, we found that elevated expression of KPNB1 correlates with unfavorable outcomes in patients with AML, and KPNB1 knockdown induces growth blocked and apoptosis in AML cells in vitro. In addition, pharmacologic inhibition of KPNB1 reduces tumor burden and extends survival in an MLL-AF9 leukemia model by KPNB1-specific inhibitor importazole (IPZ) in vivo. Moreover, KPNB1 inhibition by IPZ sensitizes AML cell lines and patients' cells to venetoclax. At the molecular level, KPNB1 directly binds to and mediates the nuclear import of HMGB2, a modulator of DNA repair. The inhibition of KPNB1 blocks the nuclear import of HMGB2 and consequently induces DNA damage in AML cells. Overall, our work elicits that inhibition of KPNB1-mediated HMGB2 nuclear translocation disrupts DNA damage repair and validates a potential target for treating AML therapy.
2025-01-08 | GSE277912 | GEO
Project description:High-risk neuroblastoma (NB) often involves amplification of the neural MYC (MYCN) oncogene as well as mutations in ALK. Currently, high-risk NB presents significant clinical challenges, and additional therapeutic options are needed. Oncogenes such as MYCN and ALK result in increased replication stress in cancer cells, offering one such therapeutically exploitable option. Here, we followed up on earlier phosphoproteomic analyses that identified ATR activity in ALK-driven NB cell lines. We tested several ATR inhibitors, identifying BAY 1895344 as the most potent inhibitor of NB cell growth and proliferation. Using RNA-Seq, proteomics and phosphoproteomics we characterized the response of NB cells and tumours to ATR inhibition, identifying key components of the DNA damage response (DDR) as well as ATRX, MYCN, E2F and DCK among other ATR targets in NB cells. ATR inhibition with BAY 1895344 also produced robust responses in mouse NB models. Remarkably, a 2 week protocol combining ATR and ALK inhibition led to complete regression of NB tumours in two independent NB genetically modified mouse tumour models. These results suggest that NB patients, particularly in high-risk groups with oncogene induced replication stress, may benefit from inhibition of ATR as therapeutic intervention.
2021-11-02 | PXD027187 | Pride
Project description:Pharmacologic inhibition of EphB3 receptor kinase ameliorates EAE
| PRJNA627447 | ENA
Project description:Metastases in the bone marrow (BM) are grim prognostic factors in patients with neuroblastoma (NB). In spite of extensive analysis of primary tumor cells from high- and low-risk NB patients, a characterization of freshly isolated BM-infiltrating metastatic NB cells is still lacking. Our aim was to identify proteins specifically expressed by metastatic NB cells, that may be relevant for prognostic and therapeutic purposes. Metastatic NB cells were freshly isolated from patients’ BM by positive immunomagnetic bead manipulation using anti-GD2 monoclonal antibody. Unselected BM samples from patients with metastatic NB were also included. Gene expression profiles were compared with those obtained from archived NB primary tumors from patients with 5y-follow-up. After validation by RT-qPCR, expression/secretion of the proteins encoded by the up-regulated genes in the BM-infiltrating NB cells was evaluated by flow cytometry and ELISA. Compared to primary tumor cells, BM-infiltrating NB cells down-modulated the expression of CX3CL1, AGT, ATP1A2 mRNAs, whereas they up-regulated several genes commonly expressed by various lineages of BM resident cells. BM-infiltrating NB cells expressed indeed the proteins encoded by the top-ranked genes, S100A8 and A9 (calprotectin), CD177 and CD3, and secreted the CXCL7 chemokine. BM-infiltrating NB cells also expressed CD271 and HLA-G. We have identified proteins specifically expressed by BM-infiltrating NB cells. Among them, calprotectin, a potent inflammatory protein, and HLA-G, endowed with tolerogenic properties facilitating tumor escape from host immune response, may represent novel biomarkers and/or targets for therapeutic intervention in high-risk NB patients.
2018-03-29 | GSE112447 | GEO
Project description:The goal of this study is to elucidate the molecular mechanism that allowed NB-1 xenograft tumors to grow out in the presence of continued ALK inhibition. Poly(A)-selected RNA was extracted from tissues of NB-1 tumors that progressed on ceritinib treatment and those treated with a vehicle to identify differentially expressed genes between these two groups.
2016-09-01 | GSE82143 | GEO
Project description:Background: Atopic dermatitis (AD) is a common inflammatory skin disease with broad impact on quality of life and on the health care system. The pathophysiology is not fully understood, but it is likely multifactorial involving immune dysfunction, altered skin barrier and environmental factors. Narrow band ultraviolet B (nb-UVB) treatment leads to normalization of the tissue and clinical improvement. However, knowledge of early changes in AD skin in response to nb-UVB is lacking and could provide important clues to decipher the disease mechanisms and potential new treatment targets. Objective: To map the early transcriptional changes in the skin in response to nb-UVB treatment. Results: When examining the early response after only three local UVB-treatments, gene expression analysis revealed 30 down- and 47 up-regulated transcripts. Among these only a small proportion were related to the inflammatory response. Interestingly, two cytokines of the interleukin (IL)-1 family were differentially expressed: the proinflammatory cytokine IL-36γ was reduced after treatment, while the anti-inflammatory cytokine IL-37 increased in skin after treatment with nb-UVB. Conclusion: Local nb-UVB induced an early decrease of the pro-inflammatory cytokine IL-36γ and an increase of the anti-inflammatory IL-37. This likely represents one of the first changes in inflammatory signaling induced by nb-UVB in atopic eczema.
2020-10-27 | GSE150797 | GEO
Project description:Effect of SMNDC1 small molecule inhibition on gene expression
| PRJNA966990 | ENA
Project description:We cultured adherent primary cell lines from NB tumor samples. Adherent primary cell lines from NB tumor samples have a subpopulation of neural crest progenitors that grow as spheres when cultured in low-binding conditions.
2016-02-25 | GSE78268 | GEO
Project description:Background: Ewing sarcoma, a highly aggressive tumor of children and young adults, is characterized most commonly by an 11;22 chromosomal translocation that fuses EWSR1 located at 22q12 with FLI1, coding for a member of the ETS family of transcription factors. Although genetic changes in Ewing sarcoma have been extensively researched, our understanding of the role of epigenetic modifications in this neoplasm is limited. Procedure: In an effort to improve our knowledge in the role of epigenetic changes in Ewing sarcoma we evaluated the in vitro antineoplastic effect of the DNA methyltransferase inhibitor 5-Aza-deoxycytidine (5-Aza-dC) and identified epigenetically silenced genes by pharmacologic unmasking of DNA methylation coupled with genome-wide expression profiling.
2014-03-05 | E-GEOD-44934 | biostudies-arrayexpress
Project description:Dr. Ladisch's work focuses on the establishment of the biological significance of gangliosides that are shed by tumor cells, particularly those involved in pediatric cancers, including brain tumors and neuroblastoma. These studies are directed toward illuminating the hypothesis that shed gangliosides enhance tumor formation, possibly both by inhibiting the antitumor immune response and by enhancing growth factor-induced signaling and proliferation of fibrobalsts and vascular endotheilial cells in the tumor microenvironment. Delineation of the signaling pathways affected by ganglioside exposure is currently under study. The effect of retinoic acid on the mRNA levels of ganglioside glycosyltransferases in neuroblastoma cells in vitro Experiment to determine mRNA expression for ganglioside glycosyltransferases in NB cells (untreated versus treated with ATRA) using the Glyco-gene Chip by the Consortium for Functional Glycomics. Human NB cell lines LAN-5 were incubated with 10 µM of all-trans retinoic acid or untreated as control, and total RNA harvested after 24 hours, 72 hours and 120 hours of exposure to retinoic acid. We performed three independent experiments on either cell line so that for each cell line and each time point three replicates were be obtained (total: 18 chips). Glycosyltransferases of particular interest are LacCer synthase, GlucCer synthase, GM3 synthase, GD3 synthase, GM2/GD2 synthase, GD1b/GM1a synthase, GT1b/GD1a synthase and GQ1b/GT1a synthase.
2011-01-07 | E-GEOD-26481 | biostudies-arrayexpress