scholarly journals Analysis of gene expression profiles as a tool to uncover tumor markers of liver cancer progression in a rat model

2014 ◽  
Vol 3 (2) ◽  
pp. 167-172 ◽  
Author(s):  
VERÓNICA R. VÁSQUEZ-GARZÓN ◽  
OLGA BELTRÁN-RAMÍREZ ◽  
MARTHA E. SALCIDO-NEYOY ◽  
NANCY CERVANTE-ANAYA ◽  
SAÚL VILLA-TREVIÑO
Keyword(s):  
Gene Expression ◽  
Liver Cancer ◽  
Tumor Markers ◽  
Cancer Progression ◽  
Rat Model ◽  
Expression Profiles ◽  
Gene Expression Profiles

scholarly journals Gene Expression and Transcriptome Profiling of Changes in a Cancer Cell Line Post-Exposure to Cadmium Telluride Quantum Dots: Possible Implications in Oncogenesis

Dose-Response ◽  
2021 ◽  
Vol 19 (2) ◽  
pp. 155932582110198
Author(s):  
Mohammed S. Aldughaim ◽  
Mashael R. Al-Anazi ◽  
Marie Fe F. Bohol ◽  
Dilek Colak ◽  
Hani Alothaid ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantum Dots ◽  
Cancer Cells ◽  
Cadmium Telluride ◽  
Cancer Progression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Dependent Manner ◽  
Cdte Qds ◽  
Cadmium Telluride Quantum Dots

Cadmium telluride quantum dots (CdTe-QDs) are acquiring great interest in terms of their applications in biomedical sciences. Despite earlier sporadic studies on possible oncogenic roles and anticancer properties of CdTe-QDs, there is limited information regarding the oncogenic potential of CdTe-QDs in cancer progression. Here, we investigated the oncogenic effects of CdTe-QDs on the gene expression profiles of Chang cancer cells. Chang cancer cells were treated with 2 different doses of CdTe-QDs (10 and 25 μg/ml) at different time intervals (6, 12, and 24 h). Functional annotations helped identify the gene expression profile in terms of its biological process, canonical pathways, and gene interaction networks activated. It was found that the gene expression profiles varied in a time and dose-dependent manner. Validation of transcriptional changes of several genes through quantitative PCR showed that several genes upregulated by CdTe-QD exposure were somewhat linked with oncogenesis. CdTe-QD-triggered functional pathways that appear to associate with gene expression, cell proliferation, migration, adhesion, cell-cycle progression, signal transduction, and metabolism. Overall, CdTe-QD exposure led to changes in the gene expression profiles of the Chang cancer cells, highlighting that this nanoparticle can further drive oncogenesis and cancer progression, a finding that indicates the merit of immediate in vivo investigation.

scholarly journals CancerLivER: a database of liver cancer gene expression resources and biomarkers

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Harpreet Kaur ◽  
Sherry Bhalla ◽  
Dilraj Kaur ◽  
Gajendra PS Raghava
Keyword(s):  
Gene Expression ◽  
Liver Cancer ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Full Potential ◽  
Individual Gene ◽  
Comprehensive Information ◽  
Tremendous Amount ◽  
Disease Specific

Abstract Liver cancer is the fourth major lethal malignancy worldwide. To understand the development and progression of liver cancer, biomedical research generated a tremendous amount of transcriptomics and disease-specific biomarker data. However, dispersed information poses pragmatic hurdles to delineate the significant markers for the disease. Hence, a dedicated resource for liver cancer is required that integrates scattered multiple formatted datasets and information regarding disease-specific biomarkers. Liver Cancer Expression Resource (CancerLivER) is a database that maintains gene expression datasets of liver cancer along with the putative biomarkers defined for the same in the literature. It manages 115 datasets that include gene-expression profiles of 9611 samples. Each of incorporated datasets was manually curated to remove any artefact; subsequently, a standard and uniform pipeline according to the specific technique is employed for their processing. Additionally, it contains comprehensive information on 594 liver cancer biomarkers which include mainly 315 gene biomarkers or signatures and 178 protein- and 46 miRNA-based biomarkers. To explore the full potential of data on liver cancer, a web-based interactive platform was developed to perform search, browsing and analyses. Analysis tools were also integrated to explore and visualize the expression patterns of desired genes among different types of samples based on individual gene, GO ontology and pathways. Furthermore, a dataset matrix download facility was provided to facilitate the users for their extensive analysis to elucidate more robust disease-specific signatures. Eventually, CancerLivER is a comprehensive resource which is highly useful for the scientific community working in the field of liver cancer.Availability: CancerLivER can be accessed on the web at https://webs.iiitd.edu.in/raghava/cancerliver.

scholarly journals Combinatorial targeting of MTHFD2 and PAICS in purine synthesis as a novel therapeutic strategy

2019 ◽  
Vol 10 (11) ◽  
Author(s):  
Chantal Hoi Yin Cheung ◽  
Chia-Lang Hsu ◽  
Chao-Yin Tsuei ◽  
Tzu-Ting Kuo ◽  
Chen-Tsung Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Cancer Progression ◽  
Expression Profiles ◽  
Neuroblastoma Cell ◽  
Neuroblastoma Cells ◽  
Gene Expression Profiles ◽  
Migration Ability ◽  
Purine Synthesis ◽  
One Carbon Metabolism

Abstract MYCN-amplified (MNA) neuroblastoma is an aggressive neural crest-derived pediatric cancer. However, MYCN is indispensable for development and transcriptionally regulates extensive network of genes. Integrating anti-MYCN ChIP-seq and gene expression profiles of neuroblastoma patients revealed the metabolic enzymes, MTHFD2 and PAICS, required for one-carbon metabolism and purine biosynthesis were concomitantly upregulated, which were more susceptible to metastatic neuroblastoma. Moreover, we found that MYCN mediated the folate cycle via MTHFD2, which contributed one-carbon unit to enhance purine synthesis, and further regulated nucleotide production by PAICS in response to cancer progression. Dual knockdown of the MYCN-targeted gene pair, MTHFD2 and PAICS, in MNA neuroblastoma cells synergically reduced cell proliferation, colony formation, migration ability, and DNA synthesis. By systematically screening the compound perturbagens, the gene expression levels of MTHFD2 and PAICS were specifically suppressed by anisomycin and apicidin across cell lines, and our co-treatment results also displayed synergistic inhibition of MNA neuroblastoma cell proliferation. Collectively, targeting a combination of MYCN-targeted genes that interrupts the interconnection of metabolic pathways may overcome drug toxicity and improve the efficacy of current therapeutic agents in MNA neuroblastoma.

scholarly journals Integrative analysis of multiple gene expression profiles applied to liver cancer study

FEBS Letters ◽  
2004 ◽  
Vol 565 (1-3) ◽  
pp. 93-100 ◽  
Author(s):  
Jung Kyoon Choi ◽  
Jong Young Choi ◽  
Dae Ghon Kim ◽  
Dong Wook Choi ◽  
Bu Yeo Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Cancer ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Integrative Analysis ◽  
Multiple Gene ◽  
Cancer Study

scholarly journals Correlation between liver cancer occurrence and gene expression profiles in rat liver tissue

2011 ◽  
Vol 10 (4) ◽  
pp. 3480-3513 ◽  
Author(s):  
C.S. Xu ◽  
G.P. Wang ◽  
L.X. Zhang ◽  
C.F. Chang ◽  
J. Zhi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Cancer ◽  
Rat Liver ◽  
Liver Tissue ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cancer Occurrence

scholarly journals Gene expression profiles of human breast cancer progression

2003 ◽  
Vol 100 (10) ◽  
pp. 5974-5979 ◽  
Author(s):  
X.-J. Ma ◽  
R. Salunga ◽  
J. T. Tuggle ◽  
J. Gaudet ◽  
E. Enright ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cancer Progression ◽  
Human Breast Cancer ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Breast Cancer Progression ◽  
Human Breast

Early Changes of Gene Expression Profiles in the Rat Model of Arterial Injury

2014 ◽  
Vol 25 (5) ◽  
pp. 789-796.e7 ◽  
Author(s):  
Anton Fedorov ◽  
Anna Kostareva ◽  
Johan Raud ◽  
Joy Roy ◽  
Ulf Hedin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rat Model ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Arterial Injury

scholarly journals Gene expression profiles of liver cancer cell lines reveal two hepatocyte-like and fibroblast-like clusters

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245939
Author(s):  
Keita Fukuyama ◽  
Masataka Asagiri ◽  
Masahiro Sugimoto ◽  
Hiraki Tsushima ◽  
Satoru Seo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Cancer ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cancer Cell Lines ◽  
Liver Cancer Cell ◽  
Study Objective

Cancer cell lines are widely used in basic research to study cancer development, growth, invasion, or metastasis. They are also used for the development and screening of anticancer drugs. However, there are no clear criteria for choosing the most suitable cell lines among the wide variety of cancer cell lines commercially available for research, and the choice is often based on previously published reports. Here, we investigated the characteristics of liver cancer cell lines by analyzing the gene expression data available in the Cancer Cell Line Encyclopedia. Unsupervised clustering analysis of 28 liver cancer cell lines yielded two main clusters. One cluster showed a gene expression pattern similar to that of hepatocytes, and the other showed a pattern similar to that of fibroblasts. Analysis of hepatocellular carcinoma gene expression profiles available in The Cancer Genome Atlas showed that the gene expression patterns in most hepatoma tissues were similar to those in the hepatocyte-like cluster. With respect to liver cancer research, our findings may be useful for selecting an appropriate cell line for a specific study objective. Furthermore, our approach of utilizing a public database for comparing the properties of cell lines could be an attractive cell line selection strategy that can be applied to other fields of research.

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