scholarly journals Comprehensive Analysis of MicroRNA and mRNA Expression in Normal and Tumorous Human Esophageal Squamous Cell Lines Using Microarray Datasets

2014 ◽  
Vol 2014 ◽  
pp. 1-3
Author(s):  
Ichiro Akagi ◽  
Osamu Ishibashi ◽  
Takeshi Matsutani ◽  
Nobutoshi Hagiwara ◽  
Akihisa Matsuda ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Cell Lines ◽  
Squamous Cell ◽  
Expression Profiling ◽  
Target Genes ◽  
Comprehensive Analysis ◽  
Limited Information ◽  
Normal Human ◽  
Microarray Datasets ◽  
Microarray Analyses

Despite the undisputed importance of altered microRNA (miRNA) expression in various cancers, there is limited information on the clinicopathologic significance of cancer-related miRNAs in esophageal squamous cell carcinoma (ESCC). Previously, it was reported that the expression of several miRNAs was dysregulated in ESCC. However, the target genes of these miRNAs have not been identified. Furthermore, additional miRNAs in humans have been discovered recently, indicating that revised miRNA and gene expression profiling for ESCC are necessary. Here, we provide datasets from microarray analyses to identify miRNA and mRNA expression comprehensively in Het-1A, a normal human esophageal squamous cell line, and three human ESCC cell lines.

scholarly journals Assessing Various Control Samples for Microarray Gene Expression Profiling of Laryngeal Squamous Cell Carcinoma

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 588
Author(s):  
Adam Ustaszewski ◽  
Magdalena Kostrzewska-Poczekaj ◽  
Joanna Janiszewska ◽  
Malgorzata Jarmuz-Szymczak ◽  
Malgorzata Wierzbicka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Epithelial Cells ◽  
Cell Carcinoma ◽  
Gene Expression Profiling ◽  
Cell Lines ◽  
Squamous Cell ◽  
Expression Profiling ◽  
Laryngeal Squamous Cell Carcinoma ◽  
Control Samples

Selection of optimal control samples is crucial in expression profiling tumor samples. To address this issue, we performed microarray expression profiling of control samples routinely used in head and neck squamous cell carcinoma studies: human bronchial and tracheal epithelial cells, squamous cells obtained by laser uvulopalatoplasty and tumor surgical margins. We compared the results using multidimensional scaling and hierarchical clustering versus tumor samples and laryngeal squamous cell carcinoma cell lines. A general observation from our study is that the analyzed cohorts separated according to two dominant factors: “malignancy”, which separated controls from malignant samples and “cell culture-microenvironment” which reflected the differences between cultured and non-cultured samples. In conclusion, we advocate the use of cultured epithelial cells as controls for gene expression profiling of cancer cell lines. In contrast, comparisons of gene expression profiles of cancer cell lines versus surgical margin controls should be treated with caution, whereas fresh frozen surgical margins seem to be appropriate for gene expression profiling of tumor samples.

Integrating microRNA and mRNA expression profiling using a novel algorithm identified a small set of unique genes upregulated in malignant pleural mesothelioma (MPM)

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e22111-e22111
Author(s):  
M. Suraokar ◽  
A. Corvalan ◽  
C. Chow ◽  
A. Gazdar ◽  
C. Moran ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Cell Lines ◽  
Expression Profiling ◽  
Tumor Tissue ◽  
Control Cell ◽  
Seed Region ◽  
Down Regulation ◽  
Total Rna ◽  
Tissue Specimens ◽  
Unique Genes

e22111 Background: We employed a global profiling strategy using miRNA microarrays in MPM cell lines and archival tumor tissue. Methods: We isolated total RNA from 4 MPM cell lines, 2 control cell lines, and 16 tissue specimens from patients with resected MPM (n=8) and normal counterpart (n=8) patients as controls. Total RNA was labeled with Cyanine 3, then hybridized with Agilent human miRNA microarray v1 slides. Results: Preliminary miRNA profiles show up-regulation of 44 versus down-regulation of 29 miRNA's in MSTO-211H cancer cells compared to HCT-4012 (pleural telomerase-transformed control). Profiling of 16 tissue specimens (8 normal vs 8 MPM) revealed down-regulation of 11 miRNA's in MPM tumor tissue. To focus on relevant miRNA that regulate genes involved in carcinogenesis and progression, we identified > 1000 unique genes using the online targetscan 4.2 program ( http://www.targetscan.org ), which predicts biological targets of miRNAs by identifying the presence of conserved 8-mer and 7-mer sites that match the seed region of each miRNA. We then explored a novel screening strategy, which combines mRNA expression dataset with the miRNA dataset, to narrow the list of relevant miRNA's. We conducted gene expression profiling on the cell lines and MPM tissue samples with Affymetrix U133 plus 2.0 chips. Bioinformatic analysis was conducted with MeV: MultiExperiment Viewer software, data reduction techniques (Correspondance Analysis), hierarchical clustering methods, and Serial Analysis for Microarray (SAM), and showed up-regulation of ∼300 genes in MPM compared to normal tissues. We then computed of the ∼300 mRNA's up-regulated in MPM only 32 are recognized by the 11 down-regulated miRNA's using the targetscan 4.2 algorithm. Most of the miRNA's regulate single messages while ∼20 % of the messages are regulated by more than 1 miRNA's. Some of these targets include Ets variant 1 and Protein kinase C - epsilon. Conclusions: This innovative approach of selecting highly relevant miRNA is feasible and enables discovery of novel genes based on their ability to be bound by single or multiple miRNA's. Validation of our profiling studies using real-time PCR and protein analysis methods will be presented. No significant financial relationships to disclose.

Overexpression of melanoma-associated antigen D4 as an independent prognostic factor in squamous cell carcinoma of the esophagus.

2014 ◽  
Vol 32 (3_suppl) ◽  
pp. 71-71
Author(s):  
Mitsuro Kanda ◽  
Hisaharu Oya ◽  
Soki Hibino ◽  
Hideki Takami ◽  
Dai Shimizu ◽  
...  
Keyword(s):  
Prognostic Factor ◽  
Mrna Expression ◽  
Cell Lines ◽  
Squamous Cell ◽  
Univariate Analysis ◽  
Independent Prognostic Factor ◽  
Protein Distribution ◽  
Rt Pcr ◽  
Carcinoma Of The Esophagus ◽  
Normal Tissues

71 Background: To pursue an urgently needed treatment target for esophageal cancer (EC), we investigated the function of the recently discovered melanoma-associated antigen (MAGE)-D4 in squamous cell EC. Methods: MAGE-D4 mRNA expression was analyzed in nine EC cell lines using quantitative reverse transcription-polymerase chain reaction (RT-PCR). In 65 surgical specimens of squamous cell EC with no prior neoadjuvant therapy, MAGE-D4 mRNA expression in EC tissues and corresponding normal tissues was analyzed and compared, and evaluated in terms of clinicopathological factors. In representative cases, MAGE-D4 protein distribution was analyzed immunohistochemically. Results: The heterogeneity of MAGE-D4 mRNA expression was confirmed in EC cell lines by quantitative RT-PCR. In surgical specimens, MAGE-D4 mRNA expression was significantly higher in EC tissues than in corresponding normal tissues (P < 0.001). Patients with the highest MAGE-D4 mRNA expression in EC tissues (top quartile, n=17) had significantly shorter overall survival than patients with low expression (2-year survival: 44% and 73%, respectively, P = 0.006). Univariate analysis identified age (≥ 65 years), lymphatic involvement and high MAGE-D4 mRNA expression as significant prognostic factors; high MAGE-D4 mRNA expression was also an independent prognostic factor in multivariable analysis (hazard ratio: 2.194; P = 0.039), and was significantly associated with Brinkman index (P = 0.008) and preoperative carcinoembryonic antigen level (P = 0.002). Immunohistochemical MAGE-D4b expression was consistent with MAGE-D4mRNA profiling. Conclusions: Our results suggest that MAGE-D4 overexpression influences tumor progression and MADE-D4 can be a prognostic marker and a potential molecular target in squamous cell EC.

scholarly journals Comprehensive analysis of β-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/β-catenin signaling

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 74 ◽  
Author(s):  
Andreas Herbst ◽  
Vindi Jurinovic ◽  
Stefan Krebs ◽  
Susanne E Thieme ◽  
Helmut Blum ◽  
...  
Keyword(s):  
Colorectal Carcinoma ◽  
Cell Lines ◽  
Target Genes ◽  
Carcinoma Cell ◽  
Comprehensive Analysis ◽  
Carcinoma Cell Lines

EZH2 Inhibitor DZNep Induces Apoptosis In Adult T-Cell Leukemia/Lymphoma Cells By BCL2 Suppression Via Regulation Of Mir-181a

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 4265-4265 ◽  
Author(s):  
Sasaki Daisuke ◽  
Hasegawa Hiroo ◽  
Taniguchi Hiroaki ◽  
Yoshitaka Imaizumi ◽  
Uno Naoki ◽  
...  
Keyword(s):  
T Cell ◽  
Cell Lines ◽  
Target Genes ◽  
Expression Profiles ◽  
Negative Regulator ◽  
T Cell Leukemia ◽  
Cell Leukemia ◽  
Adult T Cell Leukemia ◽  
Microarray Analyses ◽  
Bcl2 Expression

Abstract Background Adult T-cell leukemia/lymphoma (ATL) is a mature T-cell neoplasm originating from human T-cell leukemia virus type-1 (HTLV-1) infected cells. Its clinical behavior differs among patients and is sub-classified into 4 sub-types: smoldering and chronic as indolent subtypes, and acute and lymphoma as aggressive subtypes. Prognosis for patients with the aggressive subtypes is very poor with standard chemotherapy, thus a new therapeutic approach is urgently needed. Previously, we reported that EZH2, a part of the PRC2 complex, not only methylates histone, but also serves as a recruitment platform for DNA methyltransferases that methylate the promoter regions of target genes (tumor suppressor gene and miRNAs) and is overexpressed in ATL cells. We found that ATL cell lines were sensitive to DZNep (3-deazaneplanosin A), which has been shown to deplete EZH2 expression, and their proliferation was attenuated. In the present study, we clarified which target genes and miRNAs are involved in DZNep-induced ATL cell death. Results We performed microarray analyses using the ATL cell lines KK1, SO4, LMY1, and KOB to compare their gene expression profiles between cells treated and untreated with DZNep. The results showed that BCL2 transcripts in ATL cell lines were commonly suppressed by DZNep. In accordance with those findings, quantitative PCR analysis revealed that BCL2 transcripts were suppressed in DZNep-treated as compared to untreated ATL cell lines. We also confirmed that EZH2 and BCL2 protein expressions were clearly suppressed in the ATL cell lines by DZNep. These findings indicated that DZNep suppresses BCL2 expression at the transcriptional level in ATL cells. In addition, we performed another set of microarray analyses for miRNA expression profiles using primary ATL cells obtained from ATL patients and CD4 positive T-cells from healthy volunteers. The ATL cells showed decreased expression levels of several miRNAs, such as miR-101, miR-126, and miR-181a. Importantly, miR-181a has been shown to be regulated by EZH2, while miR-181a is a candidate negative regulator of BCL2 expression. Quantification of miR-181a transcripts to determine whether miR-181a is induced by DZNep showed that miR-181a was up-regulated in ATL cells by DZNep. These results strongly support the notion that miR-181a is suppressed by EZH2 and that BCL2 expression is regulated by miR-181a in ATL cells. Together, our findings indicate a unique apoptotic pathway of BCL2 suppression via miR181a and that the EZH2 inhibitor DZNep may become a novel therapeutic agent for ATL. Disclosures: No relevant conflicts of interest to declare.

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