scholarly journals Advanced bioinformatic analysis and pathway prediction of NSCLC cells upon cisplatin resistance

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A K M Nawshad Hossian ◽  
Fatema Tuz Zahra ◽  
Sagun Poudel ◽  
Camille F. Abshire ◽  
Paula Polk ◽  
...  
Keyword(s):  
Cholesterol Biosynthesis ◽  
A549 Cells ◽  
Bioinformatic Analysis ◽  
Rna Seq ◽  
Prolonged Incubation ◽  
Pathway Activity ◽  
Gene Dysregulation ◽  
Pathway Prediction ◽  
Bioinformatics Software ◽  
A549 Lung

AbstractThis study aims to identify pathway involvement in the development of cisplatin (cis-diamminedichloroplatinum (II); CDDP) resistance in A549 lung cancer (LC) cells by utilizing advanced bioinformatics software. We developed CDDP-resistant A549 (A549/DDP) cells through prolonged incubation with the drug and performed RNA-seq on RNA extracts to determine differential mRNA and miRNA expression between A549/DDP and A549 cells. We analyzed the gene dysregulation with Ingenuity Pathway Analysis (IPA; QIAGEN) software. In contrast to prior research, which relied on the clustering of dysregulated genes to pathways as an indication of pathway activity, we utilized the IPA software for the dynamic evaluation of pathway activity depending on the gene dysregulation levels. We predicted 15 pathways significantly contributing to the chemoresistance, with several of them to have not been previously reported or analyzed in detail. Among them, the PKR signaling, cholesterol biosynthesis, and TEC signaling pathways are included, as well as genes, such as PIK3R3, miR-34c-5p, and MDM2, among others. We also provide a preliminary analysis of SNPs and indels, present exclusively in A549/DDP cells. This study's results provide novel potential mechanisms and molecular targets that can be explored in future studies and assist in improving the understanding of the chemoresistance phenotype.

scholarly journals Toxicity and chemical transformation of silver nanoparticles in A549 lung cells: dose-rate-dependent genotoxic impact

2021 ◽  
Author(s):  
Laure Bobyk ◽  
Adeline Tarantini ◽  
David Beal ◽  
Giulia Veronesi ◽  
Isabelle Kieffer ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Silver Nanoparticles ◽  
Dose Rate ◽  
Cell Metabolism ◽  
A549 Cells ◽  
Dna Integrity ◽  
Lung Cells ◽  
Ag Nps ◽  
Rate Dependent ◽  
A549 Lung

Acute exposure of A549 cells to Ag-NPs induces stronger effects on DNA integrity, ROS level, cell metabolism and cell cycle than repeated exposure. Ag-NPs dissolves in both exposure conditions and Ag ions recombine with thiolated proteins.

scholarly journals The BET Inhibitor JQ1 Augments the Antitumor Efficacy of Gemcitabine in Preclinical Models of Pancreatic Cancer

Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3470
Author(s):  
Aubrey L. Miller ◽  
Patrick L. Garcia ◽  
Samuel C. Fehling ◽  
Tracy L. Gamblin ◽  
Rebecca B. Vance ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Dna Damage ◽  
Cholesterol Biosynthesis ◽  
Antitumor Efficacy ◽  
Rna Seq ◽  
Bet Inhibitor ◽  
Bet Inhibitors ◽  
Xenograft Models

Gemcitabine is used to treat pancreatic cancer (PC), but is not curative. We sought to determine whether gemcitabine + a BET bromodomain inhibitor was superior to gemcitabine, and identify proteins that may contribute to the efficacy of this combination. This study was based on observations that cell cycle dysregulation and DNA damage augment the efficacy of gemcitabine. BET inhibitors arrest cells in G1 and allow increases in DNA damage, likely due to inhibition of expression of DNA repair proteins Ku80 and RAD51. BET inhibitors (JQ1 or I-BET762) + gemcitabine were synergistic in vitro, in Panc1, MiaPaCa2 and Su86 PC cell lines. JQ1 + gemcitabine was more effective in vivo than either drug alone in patient-derived xenograft models (P < 0.01). Increases in the apoptosis marker cleaved caspase 3 and DNA damage marker γH2AX paralleled antitumor efficacy. Notably, RNA-seq data showed that JQ1 + gemcitabine selectively inhibited HMGCS2 and APOC1 ~6-fold, compared to controls. These proteins contribute to cholesterol biosynthesis and lipid metabolism, and their overexpression supports tumor cell proliferation. IPA data indicated that JQ1 + gemcitabine selectively inhibited the LXR/RXR activation pathway, suggesting the hypothesis that this inhibition may contribute to the observed in vivo efficacy of JQ1 + gemcitabine.

scholarly journals A Novel NFIX-STAT6 Gene Fusion in Solitary Fibrous Tumor: A Case Report

2021 ◽  
Vol 22 (14) ◽  
pp. 7514
Author(s):  
David S. Moura ◽  
Juan Díaz-Martín ◽  
Silvia Bagué ◽  
Ruth Orellana-Fernandez ◽  
Ana Sebio ◽  
...  
Keyword(s):  
Solitary Fibrous Tumor ◽  
Gene Fusion ◽  
Wide Spectrum ◽  
Bioinformatic Analysis ◽  
Fusion Partner ◽  
Rna Seq ◽  
Genomic Location ◽  
Nuclear Factor I ◽  
New Gene ◽  
Fibrous Tumor

Solitary fibrous tumor is a rare subtype of soft-tissue sarcoma with a wide spectrum of histopathological features and clinical behaviors, ranging from mildly to highly aggressive tumors. The defining genetic driver alteration is the gene fusion NAB2–STAT6, resulting from a paracentric inversion within chromosome 12q, and involving several different exons in each gene. STAT6 (signal transducer and activator of transcription 6) nuclear immunostaining and/or the identification of NAB2–STAT6 gene fusion is required for the diagnostic confirmation of solitary fibrous tumor. In the present study, a new gene fusion consisting of Nuclear Factor I X (NFIX), mapping to 19p13.2 and STAT6, mapping to 12q13.3 was identified by targeted RNA-Seq in a 74-year-old female patient diagnosed with a deep-seated solitary fibrous tumor in the pelvis. Histopathologically, the neoplasm did not display nuclear pleomorphism or tumor necrosis and had a low proliferative index. A total of 378 unique reads spanning the NFIXexon8–STAT6exon2 breakpoint with 55 different start sites were detected in the bioinformatic analysis, which represented 59.5% of the reads intersecting the genomic location on either side of the breakpoint. Targeted RNA-Seq results were validated by RT-PCR/ Sanger sequencing. The identification of a new gene fusion partner for STAT6 in solitary fibrous tumor opens intriguing new hypotheses to refine the role of STAT6 in the sarcomatogenesis of this entity.

Bioactive extracts of Ziziphus mauritiana induces apoptosis in A549 human lung epithelial carcinoma cells through the generation of reactive oxygen species

2021 ◽  
Vol 17 ◽  
Author(s):  
Om Prakash ◽  
Shazia Usmani ◽  
Amresh Gupta ◽  
Asif Jafri ◽  
Mohammad Fahad Ullah ◽  
...  
Keyword(s):  
Mtt Assay ◽  
Human Lung ◽  
A549 Cells ◽  
Carcinoma Cells ◽  
Ziziphus Mauritiana ◽  
Meoh Extract ◽  
Lung Carcinomas ◽  
Pharmacological Significance ◽  
Lung Epithelial ◽  
A549 Lung

Background: In recent years, novel metabolites isolated from botanical sources have attracted much attention for traditional and therapeutic significance. The ethnopharmacological studies suggest that Ziziphus mauritiana is a common remedy against several kinds of ailments. Objective: The current study has evaluated the MeOH extract of Ziziphus mauritiana leaves (ZME) through physicochemical, phytochemical, and chromatographic fingerprinting analysis, which displayed an array of biometabolites of pharmacological significance including flavonoids. Methods: The extract was further examined for anticancer activities which revealed promising anticancer properties against human lung epithelial carcinoma cells (A549) and induction of apoptosis impart by ROS. The oxidative stress was evaluated in terms of production and accumulation of cytosolic extent of ROS whereas anticancer perspective was determined by MTT assay, cell morphology analysis, followed by nuclear condensation for the examination of apoptosis induction. Results: Finding suggests that the MeOH extract of ZME markedly exhibited promising anticancer activity against the A549 lung epithelial carcinoma cell. The ZME was found to be most active in the MTT assay against A549 cells while it was less toxic to normal cells. The intracellular ROS generation was remarkably induced by ZME, which correlated with the ability of the flavonoid-rich fractions in the MeOH extract to inhibit cell growth and might induce apoptosis. Conclusion: The present study provides useful insight concerning the promising anticancer potential of ZME against A549 lung carcinomas. However, the clinical correlation will be required for its authorization and in the discovery of significant and least noxious novel agents against lung carcinomas.

scholarly journals Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 952 ◽  
Author(s):  
Michael I. Love ◽  
Charlotte Soneson ◽  
Rob Patro
Keyword(s):  
Software Package ◽  
Gene Expression Analysis ◽  
Real Data ◽  
Transcript Level ◽  
Bioinformatic Analysis ◽  
Rna Seq ◽  
Statistical Framework ◽  
Gene Level ◽  
Show Evidence ◽  
Differential Gene

Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Here we present a simple workflow using a set of existing R/Bioconductor packages for analysis of DTU. We show how these packages can be used downstream of RNA-seq quantification using the Salmon software package. The entire pipeline is fast, benefiting from inference steps by Salmon to quantify expression at the transcript level. The workflow includes live, runnable code chunks for analysis using DRIMSeq and DEXSeq, as well as for performing two-stage testing of DTU using the stageR package, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU. We evaluate these packages and other related packages on a simulated dataset with parameters estimated from real data.

Red Raspberry Extracts Inhibit A549 Lung Cancer Cell Migration, Invasion, and Epithelial-Mesenchymal Transition Through the Epidermal Growth Factor Receptor/Signal Transducer and Activator of Transcription-3 Signaling Pathway

2021 ◽  
Vol 11 (3) ◽  
pp. 439-444
Author(s):  
Jiayi Ren ◽  
Lifang Wang ◽  
Jia Fu ◽  
Chunyang Wang ◽  
Yan Gong ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Protein Expression ◽  
Cyclin D1 ◽  
Signaling Pathway ◽  
A549 Cells ◽  
Advanced Lung Cancer ◽  
Migration And Invasion ◽  
Red Raspberry ◽  
A549 Lung ◽  
E Cadherin

The incidence and mortality of lung cancer ranks first among all malignant tumors in the world. Because it is relatively asymptomatic at early stages, most patients do not become aware of the disease until it has progressed to an advanced stage. Advanced lung cancer metastasis results in systemic cachexia and effective treatment becomes challenging, leading to poor response and outcome. Therefore, the development of new drugs for the treatment of lung cancer is paramount. In this study, A549 cells were treated with different concentrations of red raspberry extract and the proliferation, migration, and invasion of cells were evaluated. The results indicated that red raspberry extract reduced the proliferation, migration, and invasion of A549 cells. Western blot analysis was used to detect the expression of the cyclin D1, N-cadherin, vimentin, E-cadherin, EGFR, and STAT3 proteins. Treatment with red raspberry extract reduced the expression of cyclin D1, N-cadherin, vimentin, EGFR, and STAT3, whereas the expression of E-cadherin increased. Following transfection of an EGFR overexpression vector into A549 cells, we observed a reduced inhibitory effect of the red raspberry extract on the proliferation, migration, and invasion of A549 cells. In addition, EGFR overexpression abrogated the increased expression of cyclin D1, N-cadherin, vimentin, EGFR, and STAT3 protein expression in A549 cells following extract treatment. In contrast, E-cadherin protein expression was decreased under these treatment conditions. Overall, this study suggests that red raspberry extract may reduce the proliferation, migration, invasion, and epithelialmesenchymal transition of A549 lung cancer cells by inhibiting the activation of the EGFR/STAT3 signaling pathway. These findings may lead to the development of new strategies to treat advanced lung cancer.

scholarly journals Wnt signaling mediates oncogenic synergy between Akt and Dlx5 in T-cell lymphomagenesis by enhancing cholesterol synthesis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yinfei Tan ◽  
Eleonora Sementino ◽  
Zemin Liu ◽  
Kathy Q. Cai ◽  
Joseph R. Testa
Keyword(s):  
Transcription Factor ◽  
T Cell ◽  
Cholesterol Synthesis ◽  
Regulatory Element ◽  
Cholesterol Biosynthesis ◽  
Homeobox Gene ◽  
Rna Seq ◽  
Expression Of Genes ◽  
Highly Sensitive ◽  
Sterol Regulatory Element

Abstract The Dlx5 homeobox gene was first implicated as an oncogene in a T-ALL mouse model expressing myristoylated (Myr) Akt2. Furthermore, overexpression of Dlx5 was sufficient to drive T-ALL in mice by directly activating Akt and Notch signaling. These findings implied that Akt2 cooperates with Dlx5 in T-cell lymphomagenesis. To test this hypothesis, Lck-Dlx5;Lck-MyrAkt2 transgenic mice were generated. MyrAkt2 synergized with Dlx5 to greatly accelerate and enhance the dissemination of T-lymphomagenesis. RNA-seq analysis performed on lymphomas from Lck-Dlx5;Lck-MyrAkt mice revealed upregulation of genes involved in the Wnt and cholesterol biosynthesis pathways. Combined RNA-seq and ChIP-seq analysis of lymphomas from Lck-Dlx5;Lck-MyrAkt mice demonstrated that β-catenin directly regulates genes involved in sterol regulatory element binding transcription factor 2 (Srebf2)-cholesterol synthesis. These lymphoma cells had high Lef1 levels and were highly sensitive to β-catenin and Srebf2-cholesterol synthesis inhibitors. Similarly, human T-ALL cell lines with activated NOTCH and AKT and elevated LEF1 levels were sensitive to inhibition of β-catenin and cholesterol pathways. Furthermore, LEF1 expression positively correlated with expression of genes involved in the cholesterol synthesis pathway in primary human T-ALL specimens. Together, these data suggest that targeting β-catenin and/or cholesterol biosynthesis, together with AKT, could have therapeutic efficacy in a subset of T-ALL patients.

scholarly journals Size dependent anti-invasiveness of silver nanoparticles in lung cancer cells

RSC Advances ◽  
2019 ◽  
Vol 9 (37) ◽  
pp. 21134-21138 ◽  
Author(s):  
Yu Mei Que ◽  
Xiao Qing Fan ◽  
Xiao Juan Lin ◽  
Xiao Li Jiang ◽  
Ping Ping Hu ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Silver Nanoparticles ◽  
Cancer Cells ◽  
Elevated Level ◽  
A549 Cells ◽  
Migration And Invasion ◽  
Size Dependent ◽  
Adenocarcinoma Cells ◽  
Lung Adenocarcinoma Cells ◽  
A549 Lung

Size-dependent anti-invasiveness effect of AgNPs was determined using A549 lung adenocarcinoma cells. The 13 nm AgNPs can significantly inhibit the migration and invasion of A549 cells and induce the elevated level of ROS and NF-κB directed cell apoptosis.

MG132 as a proteasome inhibitor induces cell growth inhibition and cell death in A549 lung cancer cells via influencing reactive oxygen species and GSH level

2010 ◽  
Vol 29 (7) ◽  
pp. 607-614 ◽  
Author(s):  
Yong Hwan Han ◽  
Woo Hyun Park
Keyword(s):  
Lung Cancer ◽  
Reactive Oxygen Species ◽  
Cell Cycle ◽  
Cell Death ◽  
Cancer Cells ◽  
Proteasome Inhibitor ◽  
A549 Cells ◽  
Lung Cancer Cells ◽  
Oxygen Species ◽  
A549 Lung

Carbobenzoxy-Leu-Leu-leucinal (MG132) as a proteasome inhibitor has been shown to induce apoptotic cell death through formation of reactive oxygen species (ROS). In the present study, we evaluated the effects of MG132 on the growth of A549 lung cancer cells in relation to cell growth, ROS and glutathione (GSH) levels. Treatment with MG132 inhibited the growth of A549 cells with an IC50 of approximately 20 μM at 24 hours. DNA flow cytometric analysis indicated that 0.5 ∼ 30 μM MG132 induced a G1 phase arrest of the cell cycle in A549 cells. Treatment with 10 or 30 μM MG132 also induced apoptosis, as evidenced by sub-G1 cells and annexin V staining cells. This was accompanied by the loss of mitochondrial membrane potential (MMP; Δψm). The intracellular ROS levels including O2•- were strongly increased in 10 or 30 μM MG132-treated A549 cells but were down-regulated in 0.1, 0.5 or 1 μM MG132-treated cells. Furthermore, 10 or 30 μM MG132 increased mitochondrial O2•- level but 0.1, 0.5 or 1 μM MG132 decreased that. In addition, 10 or 30 μM MG132 induced GSH depletion in A549 cells. In conclusion, MG132 inhibited the growth of human A549 cells via inducing the cell cycle arrest as well as triggering apoptosis, which was in part correlated with the changes of ROS and GSH levels. Our present data provide important information on the anti-growth mechanisms of MG132 in A549 lung cancer cells in relation to ROS and GSH.

scholarly journals ITRAQ-Based Proteomics Analysis of Triptolide On Human A549 Lung Adenocarcinoma Cells

2018 ◽  
Vol 45 (3) ◽  
pp. 917-934 ◽  
Author(s):  
Fangqiong Li ◽  
Dongxiao Zhao ◽  
Suwen Yang ◽  
Juan Wang ◽  
Qin Liu ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Lung Adenocarcinoma ◽  
Anticancer Activity ◽  
Cancer Cells ◽  
Cancer Cell ◽  
Cell Apoptosis ◽  
A549 Cells ◽  
Adenocarcinoma Cells ◽  
Lung Adenocarcinoma Cells ◽  
A549 Lung

Background/Aims: Triptolide (TP) is a diterpenoid triepoxide extracted from the traditional Chinese medical herb Tripterygium wilfordii that exerts prominent broad-spectrum anticancer activity to repress proliferation and induce cancer cell apoptosis through various molecular pathways. We previously observed that TP inhibits the progression of A549 cells and pancreatic cancer cells (PNCA-1) in vitro. However, the complex molecular mechanism underlying the anticancer activity of TP is not well understood. Methods: To explore the molecular mechanisms by which TP induces lung cancer cell apoptosis, we investigated changes in the protein profile of A549 cells treated with TP using a proteomics approach (iTRAQ [isobaric tags for relative and absolute quantitation] combined with NanoLC-MS/MS [nano liquid chromatography-mass spectrometry]). Changes in the profiles of the expressed proteins were analyzed using the bioinformatics tools OmicsBean and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and were verified using western blotting. Apoptosis and cell cycle effects were analyzed using flow cytometry. Results: TP induced apoptosis in A549 cells and blocked A549 cells at the G2/M phase. Using iTRAQ technology, we observed 312 differentially expressed proteins associated in networks and implicated in different KEGG pathways. Gene Ontology (GO) analysis showed the overviews of dysregulated proteins in the biological process (BP), cell component (CC), and molecular function (MF) categories. Moreover, some candidate proteins involved in PARP1/AIF and nuclear Akt signaling pathways or metastasis processes were validated by western blotting. Conclusion: TP exerted anti-tumor activity on non-small cell lung cancer (NSCLC) A549 lung adenocarcinoma cells by dysregulating tumor-related protein expression. Herein, we provide a preliminary study of TP-related cytotoxicity on A549 cells using proteomics tools. These findings may improve the current understanding of the anti-tumor effects of TP on lung cancer cells and may reveal candidate proteins as potential targets for the treatment of lung cancer.

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