Screening pathogenic genes in oral squamous cell carcinoma based on the mRNA expression microarray data

Ding, Yang; Liu, Pengfei; Zhang, Shengsheng; Lin, Tao; Han, Jianmin

doi:10.3892/ijmm.2018.3514

Cited by 12 publications

(14 citation statements)

References 36 publications

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“…Some functional parameters that can be deduced include regions of DNA that control normal and diseased states (functional genomics), protein–protein binding, enzyme substrate relationships, and even biochemical activity [ 127 ]. Some analytical uses are antibody arrays that, for example, can reveal altered mRNA and protein expression during cancer cell development, progression and metastasis [ 58 , 128 – 130 ]. Although this assay has relevance beyond basic science research, with even clinical applications, its main advantages are its small sample size, automation, and high sensitivity.…”

Section: Large-scale Analysis Of Genes and Proteins In Ca Cancer Resementioning

confidence: 99%

Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors

Mboge

Kota

McKenna

et al. 2018

International Journal of Medicinal Chemistry

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Carbonic anhydrases (CAs) are thought to be important for regulating pH in the tumor microenvironment. A few of the CA isoforms are upregulated in cancer cells, with only limited expression in normal cells. For these reasons, there is interest in developing inhibitors that target these tumor-associated CA isoforms, with increased efficacy but limited nonspecific cytotoxicity. Here we present some of the biophysical, biochemical, and cell based techniques and approaches that can be used to evaluate the potency of CA targeted inhibitors and decipher the role of CAs in tumorigenesis, cancer progression, and metastatic processes. These techniques include esterase activity assays, stop flow kinetics, and mass inlet mass spectroscopy (MIMS), all of which measure enzymatic activity of purified protein, in the presence or absence of inhibitors. Also discussed is the application of X-ray crystallography and Cryo-EM as well as other structure-based techniques and thermal shift assays to the studies of CA structure and function. Further, large-scale genomic and proteomic analytical methods, as well as cell based techniques like those that measure cell growth, apoptosis, clonogenicity, and cell migration and invasion, are discussed. We conclude by reviewing approaches that test the metastatic potential of CAs and how the aforementioned techniques have contributed to the field of CA cancer research.

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Section: Large-scale Analysis Of Genes and Proteins In Ca Cancer Resementioning

confidence: 99%

Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors

Mboge

Kota

McKenna

et al. 2018

International Journal of Medicinal Chemistry

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“…Among the P2Y receptor subtypes, P2Y 1 , P2Y 2, and P2Y 11 receptors are frequently studied in cancers [20]. For example, the potential role of P2Y 1 and P2Y 2 receptors in the regulation of cancer progression and pathogenesis of OSCC has been reported based on gene expression analysis [21,22]. On the other hand, it has been reported that P2Y 1 activation induces apoptosis in prostate and gastric cancer [23,24].…”

Section: Introductionmentioning

confidence: 99%

Extracellular ATP Induced S-Phase Cell Cycle Arrest via P2Y Receptor-Activated ERK Signaling in Poorly Differentiated Oral Squamous Cell Carcinoma SAS Cells

Lau

Aminuddin

Chan

et al. 2021

Life

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Extracellular ATP in the tumor microenvironment exhibits either pro- or antitumor effect via interaction with P2Y receptors, but the intracellular signaling and functional roles of P2Y receptors in oral squamous cell carcinoma (OSCC) are unclear. We aimed to study the effect of ATP on OSCC cell lines and the potential mechanisms involved. Through GEPIA dataset analysis, high expression levels of mRNA encoding P2Y receptors, the ATP-induced G protein-coupled receptors, were associated with better overall patient survival in head and neck squamous cell carcinoma. qPCR analysis showed that the poorly differentiated OSCC SAS cell line, had higher P2RY1 expression level compared to the well-differentiated H103 and H376 cell lines. Western blotting and flow cytometry analyses revealed that ATP phosphorylated ERK and elevated intracellular calcium signaling in all tested cell lines. A significant S-phase cell cycle arrest was observed in SAS, and preincubation with the MEK inhibitor PD0325901 reversed the ATP-induced S-phase arrest. We further demonstrated that ATP induced a slight reduction in cell count and colony formation yet significant apoptosis in SAS. Overall, we postulate that the ATP-induced S-phase arrest effect in SAS cells may be regulated through P2Y receptor-mediated ERK signaling, thus suggesting a potential antitumor effect of ATP via interaction with its distinct profile of P2Y receptors.

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“…Clinical research progress on risk factors related to the incidence of colon polyps. Studies have shown that adenoma carcinogenesis is the main cause of colon cancer, which accounts for more than 50% of colon cancer; when the diameter of an adenoma exceeds 2 cm, the chance of cancelation will also exceed 50% [16]. With the morphological progress of adenoma to cancer, a series of genetic changes such as inactivation of tumor suppressor genes and activation of oncogenes will occur at each stage [17].…”

Section: Introductionmentioning

confidence: 99%

Screening of Pathogenic Genes for Colorectal Cancer and Deep Learning in the Diagnosis of Colorectal Cancer

Zhang

Xing

2020

IEEE Access

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Based on complex networks and machine learning methods, this paper studies the mining of colorectal cancer treatment genes, and innovatively combines a variety of feature extraction and comparative analysis methods, from gene network features, gene attribute features, network and attribute integration The three aspects of characteristics comprehensively excavate the genetic characteristics, and demonstrate the feasibility of the study through comparative analysis from different perspectives. Constructing a colorectal cancer gene network, analyzing the changes in the network structure during the development of colorectal cancer, and mining the network characteristics of genes are the first issues to be studied in this paper. The analysis of the network structure compares the changes in the network structure of the driver genes in the Normal network and the Tumor network and the edge mechanism of the driver genes, and the distribution of the eigenvalues of the driver genes and non-driver genes in the Tumor network. During the development of colorectal cancer, the network structure of the gene has changed significantly, and the prediction results based on the network structure show better prediction results than the non-network structure. These findings are feasible for the research direction of this paper. The argument is carried out, and the relevant analysis results are also given in the article. However, the research method of the thesis is based on network research, so comparing structural features with non-structural features only shows that structural features have a good classification ability, and cannot directly explain that modeling using gene networks is better than not using gene networks. Finally, based on the random forest, the optimized classification is improved to reveal the important factors affecting the diagnosis of colorectal cancer, and then to identify the true potential colorectal cancer driver genes, providing guidance for the clinical research of colorectal cancer and driving gene mining. INDEX TERMS colorectal cancer; gene screening; diagnosis; deep learning.

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Screening pathogenic genes in oral squamous cell carcinoma based on the mRNA expression microarray data

Cited by 12 publications

References 36 publications

Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors

Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors

Extracellular ATP Induced S-Phase Cell Cycle Arrest via P2Y Receptor-Activated ERK Signaling in Poorly Differentiated Oral Squamous Cell Carcinoma SAS Cells

Screening of Pathogenic Genes for Colorectal Cancer and Deep Learning in the Diagnosis of Colorectal Cancer

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