Comparative expression analysis of carfilzomib-resistant and parental LP-1 human multiple myeloma cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE78069 | GEO | 2016/09/13
SECONDARY ACCESSION(S): PRJNA312517
REPOSITORIES: GEO
Similar Datasets
Project description:KMS-11 and KMS-34 cells were exposed to stepwise increasing concentrations of carfilzomib over a period of 18 weeks: cells adapted to growth in 4 nM carfilzomib by 4 weeks, in 6 nM in another 6 weeks and in 12 nM after a further 8 weeks. The resulting cell cultures, denoted KMS-11/Cfz and KMS-34/Cfz, respectively, retained resistance to carfilzomib even when tested after removal of selective pressure for approximately 8 weeks.
2015-07-09 | GSE69078 | GEO
Project description:KMS-11 and KMS-34 cells were exposed to stepwise increasing concentrations of carfilzomib over a period of 18 weeks: cells adapted to growth in 4 nM carfilzomib by 4 weeks, in 6 nM in another 6 weeks and in 12 nM after a further 8 weeks. The resulting cell cultures, denoted KMS-11/Cfz and KMS-34/Cfz, respectively, retained resistance to carfilzomib even when tested after removal of selective pressure for approximately 8 weeks. KMS-11/Cfz and KMS-34/Cfz cells were profiled for gene expression after 1 week of growth in the absence of carfilzomib together with parental KMS-11 and KMS-34 cells which had not been selected in the drug (triplicate samples).
2015-07-09 | E-GEOD-69078 | biostudies-arrayexpress
Project description:Carfilzomib-sensitive (AMO1) and resistant (AMO1-CFZ) MM cells were grown in RPMI-1640 medium supplemented with 10 % FBS and 0.68 mM L-glutamine, in a humidified incubator at 5% CO2 and 37 °C. The AMO1-CFZ medium was additionally added 90 nM CFZ, while the CFZ sensitive AMO1 cells were added vehicle (0.009 % DMSO) only. AMO1-CFZ was either harvested directly or grown for 1 week in CFZ free medium (vehicle only) prior to harvest. AMO1 and carfilzomib-resistant AMO1-CFZ cells were resuspended in 100 µl 1% sodium deoxycholate, 100 mM Tris-HCl pH 8.5, 10 mM tris(2-carboxyethyl)phosphine (TCEP), 40 mM chloroacetamide (CAA), heated at 90 °C for 45 min and sonicated for 10 cycles (30 s ON/30 s OFF) using a Bioruptor pico sonicator. After centrifugation at 16000 × g for 10 min, 50 µg soluble protein from each sample was added 100 µl 0.1M ammonium bicarbonate, 0.5 µg trypsin and digested overnight at 37°C. Peptides were desalted using C18 spin columns, dried in a speedvac centrifuge and resuspended in 0.1% formic acid prior to MS analysis. Label-free quantitatative (LFQ) LC-MS/MS was performed on a timsTOF Pro (Bruker Daltonics) connected to a nanoElute (Bruker Daltonics) HPLC. Peptides were separated over a Bruker PepSep C18 (75 µm × 15 cm) column with running buffers A (0.1 % formic acid) and B (0.1 % formic acid in acetonitrile) using a 100 min gradient from 2 % B to 40 % B. The timsTof instrument was operated in the DDA PASEF mode with 10 PASEF scans per acquisition cycle and accumulation and ramp times of 100 ms each. The ‘target value’ was set to 20000 and dynamic exclusion was activated and set to 0.4 min. The quadrupole isolation width was set to 2 Th for m/z < 700 and 3 Th for m/z > 800.
2024-06-07 | PXD045439 | Pride
Project description:Analysis of steady-state mRNA levels in liposarcoma cells treated for 28 hr with 0.05% DMSO or 10 uM Nutlin3R and/or 12.5 nM Carfilzomib
2023-05-12 | GSE226530 | GEO
Project description:Carfilzomib has a good effect in treating multiple myeloma, but more and more clinical studies have shown that the drug can cause cardiac toxicity during use, but the mechanism of action is unclear. This study aimed to comprehensively elucidate the mechanism of CFZ-induced cardiomyopathy by constructing a C57BL/6 mouse model and combining cell experiments. The research results showed that the hearts of mice treated with CFZ appeared significantly enlarged, and the cardiac function indicators decreased. The serum enzyme LDH, AST, and CK-MB levels significantly increased, suggesting severe myocardial injury. RNA extraction and QPCR detection of the heart showed that the expression of heart hypertrophy and fibrosis markers increased. Meanwhile, histological staining found that there were fewer cardiomyocytes, damaged myofibrils, and cardiac fibrosis. In the cell experiments, CFZ treatment caused the release of more LDH from rat cardiomyocytes and H9C2 cells, increased CASPASE 3/7 activity, abnormal cell morphology, enlarged cell size, myocardial hypertrophy and fibrosis marker gene expression in cardiomyocytes. Through the study of the SUMOYLATION pathway, it was found that CFZ's effects on cardiomyocyte structure and function were related to the expression of SENP genes, especially SENP1, which showed a significant downregulation in cardiomyocytes and mouse heart tissue, and was positively correlated with the levels of cardiac injury marker genes. This study further explored the mechanism of action by specifically altering the expression of SENP1 in cardiomyocytes. The results show that the knockdown of SENP1 in cardiomyocytes leads to more severe myocardial damage after CFZ treatment, suggesting that the expression of SENP1 can potentially affect the cardiotoxicity caused by CFZ. Further, by using silver staining and mass spectrometry to identify the interacting proteins with SENP1 after CFZ treatment, we found that the knockdown of DDX17 had a similar myocardial injury effect as SENP1. Subsequently, through Co-IP, protein stability experiments, and ubiquitination analysis experiments, we determined that SENP1 can maintain the protein stability of DDX17 by inhibiting its SUMO modification, thereby preventing cardiomyocyte injury and apoptosis. We hope to provide a new perspective and potential cardioprotective strategy for clinical use.
2024-08-10 | GSE273971 | GEO
Project description:Bortezomib (BTZ), Carfilzomib (CFZ) and Ixazomib (IXA) are proteasome inhibitors (PI) approved for Multiple Myeloma (MM) treatment. By design, they all target the rate-limiting proteasome beta 5 (B5) subunit. CFZ treatment increases the survival of patients with relapsed/refractory MM compared to BTZ but is associated with heart failure not commonly observed for BTZ. The molecular basis for CFZ-induced cardiotoxicity is poorly understood. We time to investigate the transcriptomic effects of acute proteasome inhibition in the murine heart.
2023-07-01 | E-MTAB-11028 | biostudies-arrayexpress
Project description:Lp(a) and its distinguishing apolipoprotein constituent apo(a) have been shown to elicit proinflammatory responses from monocytes and macrophages. To obtain a global picture of the effect of Lp(a) and apo(a) on the transcriptome of these cells, we treated THP-1 macrophages with 250 nM Lp(a) or apo(a) for 6 hours, harvested RNA from the cells, and then performed RNA-seq using an Illumina NextSeq instrument. Analysis of the data using GO and KEGG strategies revealed a series of proinflammatory genes upregulated by apo(a) and even more dramatically by Lp(a).
2023-05-08 | GSE226759 | GEO
Project description:Hepatocellular carcinoma (HCC) ranks among one of the most prevalent and lethal cancers affecting humans. Currently, there are limited effective treatments available for HCC. In the search for potential anti-HCC agents, we found that carfilzomib, a proteasome inhibitor, exerts anti-HCC activities. However, the underlying mechanisms of action are main unclear. In this study, we evaluated the effectiveness of carfilzomib against HCC capability and explored its underlying mechanisms. Cell Counting Kit 8 (CCK8), EdU (5-ethynyl-2-deoxyuridine) staining, and colony formation assays were employed to analyze the antiproliferative ability of carfilzomib on MHCC-97H and Huh7 cells. Additionally, flow cytometry was used to assess the effect on the cell cycle. Western blotting was utilized to examine the protein expression levels associated with cell cycle arrest. Furthermore, short hairpin RNA (shRNA) transfection was used to investigate the role of GADD45a (growth arrest and DNA damage 45a) on carfilzomib-induced cell cycle arrest. A xenograft tumor model using nude mouse was employed to evaluate the anti-HCC activity of carfilzomib in vivo. The finding demonstrated that carfilzomib inhibited the proliferation, invasion, and migration in both MHCC-97H and Huh7 cells. In addition, carfilzomib caused cell cycle arrest by suppressing the expression of cyclin A1, cyclin E1, cyclin-dependent kinases 2 (CDK2), and cyclin-dependent kinases 4 (CDK4). It also upregulated the expression of GADD45a, and inhibition of GADD45a through shRNA abolished carfilzomib-induced cell cycle arrest in HCC cells. Importantly, carfilzomib demonstrated its ability to inhibit the Huh7 cell growth in vivo. Our research has revealed, for the first time, that carfilzomib inhibited the progression of HCC cells by upregulating GADD45a expression. These findings suggest that carfilzomib could be a potential chemotherapeutic agent against HCC.
2024-12-18 | GSE284346 | GEO
Project description:All-trans retinoic acid (ATRA) is important for sensitizing MM cells to carfilzomib (Cfz). To determine what signalling pathways are affected by ATRA in Cfz-treated MM cells, MM.1S MM cell line was pulsed with Cfz and then cultured with DMSO or 10µM ATRA for 12 h. Total RNAs of 2 x 106 MM.1S cells were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Gene Expression and Genotyping Facility at Case Western Reserve University (Cleveland, OH) for genearray followed by data analysis. We use microarray data to determine differential expression of genes in Cfz-treated MM cells in culture with DMSO and ATRA.
2021-01-01 | GSE153196 | GEO
Project description:Purpose: Evaluate the molecular changes associated with Cfz -induced cardiotoxicity Methods: RNA-Seq analysis was performed to analyze global transcriptome profiles of hiPSC-CMs treated with DMSO (Control group), 1 µM Carfilzomib ( Cfz group). The Illumina TruSeq technology was used to prepare RNA-Seq libraries, and next-generation sequencing was done via an Illumina HiSeq 2000. RNA sequence reads were aligned to the human reference genome (GRCh38) using STAR v2.5. HTSeq v0.6.1 was used to count the read numbers mapped of each gene, and then Fragments Per Kilobase Million (FPKM) was calculated to estimate gene abundance. Differential expression analysis was performed using the DESeq2 R package (2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg's approach. As detected by RNA-Seq, some differential genes regulated by Cfz were significantly involved in cardiac contraction and extracellular matrix (ECM). Among the top 10 up-regulated genes post Cfz treatment,most of thoese genes was related to the heat shock protein expression( HSPA1B,HSPA6,,HSPH1, BAG3). And among the top 10 down-regulated genes post Cfz treatment, some correlated to contraction and Extra cellular matrix ( ITG11, SLC9A3, TNN1) . Conclusion: Carfilzomib -induced alteration of hiPSC-CM transcriptomic profiles. Enhanced HSPs and down regulate cardiac related contraction gene and extracellular matrix.
2021-10-04 | GSE163102 | GEO