Microtubule Affinity-Regulating Kinase 2 is associated with DNA damage response and cisplatin resistance in non-small cell lung cancer.
ABSTRACT: MARK2 expression is associated with the malignant phenotype, expression of DNA repair components, NF-κB inhibition and cell cycle transcription factors in lung cancer cells We used microarrays to determine the global gene expression pattern associated with knockdown of MARK2 3 lung cancer cell lines overexpressing MARK2 have been selected to assess the gene expression pattern after MARK2 knockdown. RNA extraction and hybridization on Affymetrix microarrays have been done on 2 biological replicates for each line (H1993, H1693 and H1650) after shRNA lentiviral transduction and compared with respective contols using the empty vector pLKO.
Microtubule affinity-regulating kinases (MARKs) are involved in several cellular functions but few studies have correlated MARK kinase expression with cancer, and none have explored their role in lung cancer. In this study, we identified MARK2 as frequently disrupted by DNA hypomethylation and copy gain, resulting in concordant overexpression in independent lung tumor cohorts and we demonstrate a role for MARK2 in lung tumor biology. Manipulation of MARK2 in lung cell lines revealed its involvem ...[more]
Project description:Application of cisplatin (DDP) for treating lung cancer is restricted due to its toxicity and drug resistance. In this study, we aimed to examine whether Jinfukang (JFK), an effective herbal medicine against lung cancer, enhances DDP-induced cytotoxicity in lung cancer cells. Morphologically, we observed JFK increases DDP-induced pro-apoptosis in A549 cells in a synergistic manner. Transcriptome profiling analysis indicated that combination of JFK and DDP regulates genes involved in apoptosis-related signaling pathways. Moreover, we found the combination of JFK and DDP produces synergistic pro-apoptosis effect in other lung cancer cell lines NCI-H1975, NCI-H1650 and NCI-H2228. Particularly, we demonstrated AIFM2 is activated by the combined treatment of JFK and DDP, and partially mediate the synergistic pro-apoptosis effect. Collectively, this study gives the first evidence that activation of AIFM2 contributes to induction of pro-apoptosis by combined treatment with JFK and DDP in human lung cancer cells and provides an insight for its potential clinical application in lung cancer treatment.
Project description:Identification of a AMPK-relevant gene network hierarchy based on transcriptome data upon gene knockdown Overall design: Knockdown of 20 genes in H1650 cell line following transcriptome analyses
Project description:Ganoderma colossum (Fr.) Baker, a white rot fungus distributed in tropical and subtropical forests, is a rare Ganoderma mushroom belonging to the family Ganodermataceae. In Asia, the fruiting body of G. colossum has been used as tonics or as folk medicine for a variety of illnesses, including malignant diseases. Colossolactone H (colo H) as a new compound was isolated and studied for its anticancer mechanism in human lung cancer H1650 cells. We used microarrays to analyze the gene expression changes upon colo H treatment that helped underlying the molecular mechanism of colo H in H1650 lung cancer cells. The H1650 cells treated with colo H for 12 and 24 h for RNA extraction and hybridization on Affymetrix microarrays.
Project description:We profiled basal and bicuculline+4-AP inducible mRNA expression in cultured mouse hippocampal neurons with or without viral shRNA mediated knockdown of Kdm6b We harvested mRNA from neurons under four conditions (pLKO vector/treatment control, pLKO vector/3hr bicuculline+4AP, Kdm6b knockdown/treatment control,Kdm6b knockdown/3hr bicuculline+4AP). Libraries were generated and used for RNA sequencing.
Project description:Transcriptional profiling of SAS cells transfected with pLKO.1-LYRIC shRNA-B expression vector (desinaged as B) and control SAS cells (transfected with pLKO.1 vector, designated as CTL). Goal was to determine the effects of LYRIC knockdown on global SAS cells gene expression. Two-condition experiment, SAS cells transfected with pLKO.1-LYRIC shRNA-B expression vector (desinaged as B) v.s. control SAS cells (transfected with pLKO.1 vector, designated as CTL). Biological replicates: 4 control replicates, 4 transfected replicates.
Project description:PTEN or GFP were stably expressed in PTEN-deficient lung adenocarcinoma cells by viral transfection followed by puromycin selection. Microarray analysis of total RNA isolated from H1650 cells stably expressing PTEN or GFP was performed to identify potential PTEN responsive genes. Overall design: Three biological replicate retroviral infections of H1650 cells were performed with pBABE-PTEN or pBABE-GFP expression plasmidsollowed by selection in 2 ug/ml puromycin for 2 days. Stable PTEN expression was confirmed by immunoblot analysis 5 days post-infection. Total RNA was isolated from each replicate using the RNeasy kit (Qiagen) according to manufacturer’s instructions. After quality control validation, total RNA was processed for labeling and hybridization on GeneChip Human Genome Arrays (HGU133 plus 2.0) followed by scanning and image quantification.
Project description:CDK8 Mediator kinase is amplified and overexpressed in colon cancers; elevated CDK8 expression is associated with shorter patient survival. Nevertheless, CDK8 kinase inhibitors do not generally suppress colon cancer growth. We addressed this paradox by investigating the effects of CDK8 knockdown or a CDK8 kinase inhibitor on tumor growth at primary and metastatic sites. CDK8 knockdown or inhibition had no significant effect on primary tumors but suppressed the growth of hepatic metastases in murine and human colon cancer models. The effect of CDK8 inhibition on liver metastasis is mediated by upregulation of matrix metalloproteinase (MMP) inhibitor TIMP3 and downregulation of several MMPs. Overall design: Transcriptomic comparison between CT26-pLKO.1 and CT26-shCDK8 cells were performed using Illumina MouseWG-6 v2.0 microarrays by the Hollings Cancer Center Genomics Shared Resource facility at Medical University of South Carolina.
Project description:Analysis of gene expression altered upon knockdown of Siah2 in prosate cancer cells. The objective is to elucidate which signaling pathways or transcription factors are regulated by the E3 ubiquitin ligase Siah2 in human prostate cancer cells. CWR22Rv1 cells were in fected with pLKO.1 control or Siah2 shRNA, and selected with 1ug/ml of puromycin to get stable transfectants. Total RNA was extracted for micorarray analysis to compare the diffentially expressed genes between pLKO.1 control and Siah2 knockdown cells.
Project description:Earlier studies had shown that side population cells isolated from established non-small cell lung cancer (NSCLC) cell lines exhibit cancer stem cell properties. Microarray data from side population (SP) and main population (MP) cells isolated from 4 NSCLC lines (A549, H1650, H460, H1975) were used to examine gene expression profiles associated with stemness. Total RNA extracted from SP and MP samples were used to generate cRNA targets, which were hybridized to Human Genome U133 Plus 2.0 probe arrays. Raw data was processed and the mean center expression level for each gene was determined. Four cell lines (A549, H1650, H460, H1975), each having 1 SP and 1 MP sample.
Project description:CDK8 Mediator kinase is amplified and overexpressed in colon cancers; elevated CDK8 expression is associated with shorter patient survival. Nevertheless, CDK8 kinase inhibitors do not generally suppress colon cancer growth. We addressed this paradox by investigating the effects of CDK8 knockdown or a CDK8 kinase inhibitor on tumor growth at primary and metastatic sites. CDK8 knockdown or inhibition had no significant effect on primary tumors but suppressed the growth of hepatic metastases in murine and human colon cancer models. The effect of CDK8 inhibition on liver metastasis is mediated by upregulation of matrix metalloproteinase (MMP) inhibitor TIMP3 and downregulation of several MMPs. Overall design: Microarray analysis comparing CT26 cells treated with DMSO and 5 µM Senexin B for 24 h and the comparison between CT26-pLKO.1 and CT26-shCDK8 were performed using Affymetrix Mouse gene 2.0 X ST arrays by the Functional Genomics Core of the Center for Targeted Therapeutics at the University of South Carolina.