UGT2B17 knock down in chronic lymphocytic leukemia cell line MEC-1
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE38367 | GEO | 2015/05/01
SECONDARY ACCESSION(S): PRJNA167749
REPOSITORIES: GEO
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Project description:Comparison of gene expression after stable shRNA induced knock down of UGT2B17 and scrambled shRNA in the cell line model MEC-1. Transfection was performed using lentiviral particles, RNA was harvested after culture for 2 weeks. Results provide insight into functional UGT2B17 involvement in CLL cells. Knock down of UGT2B17 in comparison to scrambled shRNA in three independent replicates each.
2015-05-01 | E-GEOD-38367 | biostudies-arrayexpress
Project description:This work shows that signaling-lymphocytic-activation-molecule-1 (SLAMF1), a co-stimulatory molecule and a microbial sensor, is expressed by normal CD19+/CD5+ B-lymphocytes. Its expression is lost in a subset of patients with chronic lymphocytic leukemia (CLL) characterized by an aggressive form of the disease, with shorter time to first treatment and overall survival. Silencing of SLAMF1 in the CLL-like Mec-1 cell line (constitutively SLAMF1+) modulated pathways connected to cell migration, cytoskeletal organization and intracellular vesicle formation/recirculation. Loss of SLAMF1 was associated to increased expression of CXCR4, CD38 and CD44, positively affecting chemotactic responses to CXCL12. Ligation of SLAMF1 with an agonistic monoclonal antibody promoted the autophagic flux, by increasing reactive oxygen species (ROS) accumulation and inducing phosphorylation of p38, JNK1/2 and bcl-2. The direct consequence was the assembly of the autophagy macro-complex that included SLAMF1, the scaffold protein Beclin1 and the enzyme Vps34. Consistently, SLAMF1-silenced cells or SLAMF1low primary CLL cells were resistant to autophagy-activating therapeutic agents, such as fludarabine or the BH3 mimetic ABT-737. These results indicate that loss of SLAMF1 expression modulates genetic pathways regulating chemotaxis and autophagy and potentially affecting drug responses, thus providing a likely explanation for the unfavorable clinical outcome experienced by this patient subset. Microarrays were performed comparing genetic signature of CLL-like Mec-1 cell line (constitutively SLAMF1+), transfected with a non-effective (scrambled) shRNA cassette (TR30013) used as control, and a Mec-1 variant generated silencing SLAMF1 gene using pGFP-V-RS construct for SLAMF1 shRNA (TG309422). For each cell line variants, grown in vitro in complete medium, three biological replicates were included in the chip.
2015-05-23 | E-GEOD-69165 | biostudies-arrayexpress
Project description:Stable knockdown of NET1, a RhoGEF, was achieved in AGS Gastric Cancer cells. This gene is known to be overexpressed in the disease. Knockdown was achieved using lentiviral shRNA particles. Gene expression was compared between knockdown and scrambled shRNA treated control cells. Cells were treated with and without LPA, a known activator of RhoA.
2011-01-02 | GSE26309 | GEO
Project description:Purpose: Nucleolar and spindle associated protein 1 (NUSAP1), serves as a microtubule binding protein in chromosome separation, spindle assembly, and plays significant role to ensure normal regulation of cell cycle as well. This experiment aimed to document the NUSAP1 expression and functions in chronic lymphocytic leukemia (CLL). Methods: Lentivirus vectors either encoding shNUSAP1 or empty lentiviral vector were stably transfected into MEC-1 cells. 3 shNUSAP1 transfected and 3 shControl transfected MEC-1 cell samples were performed RNA sequencing (RNA-seq) analysis, functional enrichment analyses of gene ontology (GO) and gene set enrichment analysis (GSEA). Results: Silencing NUSAP1 inhibited the cell proliferation, promoted cell apoptosis and G0/G1 phase arrest. Mechanistically, high expression of NUSAP1 strengthened DNA damage repairing with RAD51 engagement. Our results also indicated that NUSAP1 knockdown suppressed the growth of CLL cells in vivo. Conclusion: Our research investigates the mechanism by which NUSAP1 enhances chemoresistance via DNA damage repair signaling by stabilizing RAD51 in CLL cells. Hence, NUSAP1 may be expected to be a perspective target for the treatment of CLL with chemotherapy resistance.
2021-10-08 | GSE185467 | GEO
Project description:In order to evaluate the impact of PCYOX1 deletion on adipogenesis, we applied a label-free mass spectrometry-based proteomic approach to compare the proteome of 3T3-L1 differentiated for 9 days to adipocytes after PCYOX1 gene silencing. Pcyox1 was silenced using shRNA lentiviral particles. Control cells were treated with shRNA lentiviral particles containing a negative construct.
2023-05-10 | PXD039943 | Pride
Project description:To investigate Toll-like receptors (TLR) signaling in Chronic lymphocytic leukemia (CLL) cell lines, we analyzed HG-3, MEC-2 and PCL-12 CLL cell lines before and after TLR9 stimulation by RNA-sequencing followed by bioinformatic analyses and validation experiments.
2023-09-19 | GSE233595 | GEO
Project description:Fanconi anemia (FA) is a genetic disorder characterized by congenital abnormalities, bone marrow failure and increased susceptibility to cancer. Of the fifteen FA proteins, Fanconi anemia group C (FANCC) is one of eight FA core complex components of the FA pathway. Unlike other FA core complex proteins, FANCC is mainly localized in the cytoplasm, where it is thought to function in apoptosis, redox regulation, cytokine signaling and other processes. Previously, we showed that regulation of FANCC involved proteolytic processing during apoptosis. To elucidate the biological significance of this proteolytic modification, we searched for molecular interacting partners of proteolytic FANCC fragments. Among the candidates obtained, the transcriptional corepressor protein C-terminal binding protein-1 (CtBP1) interacted directly with FANCC and other FA core complex proteins. Although not required for stability of the FA core complex or ubiquitin ligase activity, CtBP1 is essential for proliferation, cell survival and maintenance of chromosomal integrity. Expression profiling of CtBP1-depleted and FA-depleted cells revealed that several genes were commonly up- and down-regulated, including the Wnt antagonist Dickkopf-1 (DKK1). These findings suggest that FA and Wnt signaling via CtBP1 could share common effectors. HeLa cell line was grown in DMEM media supplemented with 10% FBS and were incubated in 5% CO2 at 37°C. A four-plasmid (pRSV-Rev, pMDLg/pRRE, pMD2.G and pLKO.1) expression system was used for lentiviral production. Different pLKO.1 plasmids carrying shRNAs targeting FANCA, FANCD2, CtBP1 or CtBP2 or a lentiviral control vector pLKO.1-scrambled were used. Lentiviral particles were produced via calcium phosphate-mediated transient transfection of the four plasmids into HEK293T cells. Cells were exposed to appropriate lentiviral particles. In each experiment, HeLa cells were transduced for 6 hours with filtered supernatant containing recombinant lentiviral particles. After transduction, the cells were cultured for 72 hours. Total RNA extracts from 3 different samples of each scrambled, CtBPs and FANCD2 shRNA treated HeLa cells were subjected to gene expression profiling via microarray analysis. Gene expression profiles were determined with Affymetrix GeneChip® Human Gene 1.0.
2013-04-05 | E-GEOD-43330 | biostudies-arrayexpress
Project description:Stable knockdown of NET1, a RhoGEF, was achieved in AGS Gastric Cancer cells. This gene is known to be overexpressed in the disease. Knockdown was achieved using lentiviral shRNA particles. Gene expression was compared between knockdown and scrambled shRNA treated control cells. Cells were treated with and without LPA, a known activator of RhoA. Three distinct cell lines were used in this study (all AGS cells); (i) Non Target cell (NT) stably expressing non targetting shRNA (ii) 63 and (iii) 65; the latter two are stable NET1 knockdown cells and are seperatly transduced with separate NET1 targetting shRNA particles. Cells were treated with and without 10microM LPA for 4 hr. Experimental replicates were performed for each treatment (A & B), RNA was prepared from each and seperatly hybridised to U133A arrays.
2011-01-02 | E-GEOD-26309 | biostudies-arrayexpress
Project description:Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of malignant CD5+ B lymphocytes (CLL cells) in the peripheral blood, and their progressive infiltration in lymphoid organs. MMP-9 plays an important role in cell migration and survival, contributes to CLL pathogenesis by proteolytic and non-proteolytic mechanisms and may constitutive a therapeutic target. We used Affimetrix microarray technology to characterize the global gene expression profile of chronic lymphocytic leukemia (CLL) cells upon MMP-9 transfection. The aim was to establish whether MMP-9 regulates gene expression and to identify new therapeutic targets in CLL.
2016-03-21 | GSE78174 | GEO
