Analysis of global gene expression profiles suggests a role of acute inflammation in type 3C diabetes mellitus caused by pancreatic ductal adenocarcinoma

Abstract Background: Pancreatic cancer has many pathologic types, among which pancreatic ductal adenocarcinoma (PDAC) is the most common one. Bioinformatics has become a very common tool for the selection of potentially pathogenic genes. Methods: Three data sets containing the gene expression profiles of PDAC were downloaded from the gene expression omnibus (GEO) database. The limma package of R language was utilized to explore the differentially expressed genes (DEGs). To analyze functions and signaling pathways, the Database Visualization and Integrated Discovery (DAVID) was used. To visualize the protein-protein interaction (PPI) of the DEGs ,Cytoscape was performed under the utilization of Search Tool for the Retrieval of Interacting Genes (STRING). With the usage of the plug-in cytoHubba in cytoscape software, the hub genes were found out. To verify the expression levels of hub genes, Gene Expression Profiling Interactive Analysis (GEPIA) was performed. Last but not least, UALCAN analysis online tool was implemented to analyze the overall survival. Results: The 376 DEGs were highly enriched in biological processes including signal transduction, apoptotic process and several pathways, mainly associated with Protein digestion and absorption and Pancreatic secretion pathway. The expression levels of nucleolar and spindle associated protein 1 (NUSAP1) and SHC binding and spindle associated 1 (SHCBP1) were discovered highly expressed in pancreatic ductal adenocarcinoma tissues. NUSAP1 and SHCBP1 had a high correlation with prognosis. Conclusions: The findings of this bioinformatics analysis indicate that NUSAP1 and SHCBP1 may be key factors in the prognosis and treatment of pancreatic cancer.

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Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers

Annals of Oncology ◽

10.1093/annonc/mdx378.008 ◽

2017 ◽

Vol 28 ◽

pp. v451

Author(s):

O. Caba ◽

A.L. Irigoyen ◽

C. Jimenez-Luna ◽

M. Benavides ◽

F.M. Ortuño ◽

...

Keyword(s):

Gene Expression ◽

Pancreatic Ductal Adenocarcinoma ◽

Expression Profiles ◽

Meta Analysis ◽

Gene Expression Profiles ◽

Ductal Adenocarcinoma ◽

Diagnostic Biomarkers

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Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers

PLoS ONE ◽

10.1371/journal.pone.0194844 ◽

2018 ◽

Vol 13 (4) ◽

pp. e0194844 ◽

Cited By ~ 9

Author(s):

Antonio Irigoyen ◽

Cristina Jimenez-Luna ◽

Manuel Benavides ◽

Octavio Caba ◽

Javier Gallego ◽

...

Keyword(s):

Gene Expression ◽

Pancreatic Ductal Adenocarcinoma ◽

Expression Profiles ◽

Meta Analysis ◽

Gene Expression Profiles ◽

Ductal Adenocarcinoma ◽

Diagnostic Biomarkers

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Analysis of the Effect On the Expression of Global Gene Expression Profiles in Lymphocyte Subpopulations Treated by Extracorporeal Photopheresis

Blood ◽

10.1182/blood.v120.21.4841.4841 ◽

2012 ◽

Vol 120 (21) ◽

pp. 4841-4841

Author(s):

Robert M Knobler ◽

Ulrike Just ◽

Gabriele Klosner ◽

Florian Klinglmueller ◽

Martin Bilban ◽

...

Keyword(s):

Gene Expression ◽

Lymphocyte Subsets ◽

Expression Profiles ◽

Chronic Gvhd ◽

Gene Expression Profiles ◽

Global Gene Expression ◽

Extracorporeal Photopheresis ◽

Cd4 Cells ◽

Before And After

Abstract Abstract 4841 Introduction After the initial introduction of extracorporeal photopheresis (ECP) for the therapy of Sezary syndrome (CTCL) it has been found to have significant clinical effect on other T-cell mediated diseases including graft-versus-host disease (GvHD), organ transplant rejection, systemic sclerosis and other autoimmune disorders. To obtain information about modifications in gene expression patterns before and after ECP and to define gene sets with important changes in expression we analysed gene expression profiles in major lymphocyte subsets of patients before and after treatment with 8-methoxypsoralen (8-MOP) and ultraviolet A (UVA) irradiation. Patients, Materials, and Methods For this initial study 6 female patients suffering from chronic GvHD under treatment with ECP were included. Affymetrix® Human Genome U133 Plus 2.0 Arrays were used to compare global gene expression profiles in CD4+ and CD8+ lymphocytes before and after ECP. Lymphocyte subsets were isolated before and immediately after exposure to 8-MOP/UVA during a standard ECP treatment cycle. Total RNA was isolated from each cell sample and processed and analyzed according to standard procedures. Results Preliminary data suggest a significant effect in CD4+ and CD8+ lymphocytes in patients with chronic GvHD on gene transcription after 8-MOP/UVA exposure. In CD4+ cells 20 times more gene transcription can be detected when compared to CD8+ cells. These findings underline the possible key role of CD4+ cells in the mechanisms of action of ECP. Recent research in animal models found evidence for a role of CD4+ regulatory T cells in the immunomodulatory activity of ECP. Conclusion The scientific approach of this study has the advantage of exploring global gene regulatory effects of ECP without any experimental bias based on earlier evidence or on a mechanistic hypothesis. Its results offer the advantage of finding new and so far unexplored effects of ECP on the treated cells; information which should be able to generate significant data to help define key targets for subsequent research into the mechanism of action of ECP. Disclosures: No relevant conflicts of interest to declare.

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Abstract A51: Using single-cell gene expression profiles to determine the cellular landscape of pancreatic ductal adenocarcinoma

10.1158/1538-7445.panca19-a51 ◽

2019 ◽

Author(s):

Veerin R. Sirihorachai ◽

Samantha B. Kemp ◽

Marina Pasca Di Magliano

Keyword(s):

Gene Expression ◽

Single Cell ◽

Pancreatic Ductal Adenocarcinoma ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Ductal Adenocarcinoma ◽

Cell Gene Expression ◽

Cell Gene

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Identification of gene expression profiles in pancreatic ductal adenocarcinoma. Clinical implications

Pancreatology ◽

10.1016/j.pan.2013.07.015 ◽

2013 ◽

Vol 13 (4) ◽

pp. e5

Author(s):

M.C. Gómez Mateo ◽

L. Sabater Ortí ◽

J.F. Chaves Martínez ◽

A.B. García García ◽

J. Sastre Belloch ◽

...

Keyword(s):

Gene Expression ◽

Pancreatic Ductal Adenocarcinoma ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Ductal Adenocarcinoma ◽

Clinical Implications

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Identify key genes and pathways in pancreatic ductal adenocarcinoma via bioinformatics analysis

10.21203/rs.3.rs-19826/v1 ◽

2020 ◽

Author(s):

Huatian Luo ◽

Da-qiu Chen ◽

Jing-jing Pan ◽

Zhang-wei Wu ◽

Can Yang ◽

...

Keyword(s):

Gene Expression ◽

Pancreatic Cancer ◽

Pancreatic Ductal Adenocarcinoma ◽

Bioinformatics Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Gene Expression Omnibus ◽

Ductal Adenocarcinoma ◽

Hub Genes ◽

Expression Levels

Abstract Background: Pancreatic cancer has many pathologic types, among which pancreatic ductal adenocarcinoma (PDAC) is the most common one. Bioinformatics has become a very common tool for the selection of potentially pathogenic genes.Methods: Three data sets containing the gene expression profiles of PDAC were downloaded from the gene expression omnibus (GEO) database. The limma package of R language was utilized to explore the differentially expressed genes (DEGs). To analyze functions and signaling pathways, the Database Visualization and Integrated Discovery (DAVID) was used. To visualize the protein-protein interaction (PPI) of the DEGs ,Cytoscape was performed under the utilization of Search Tool for the Retrieval of Interacting Genes (STRING). With the usage of the plug-in cytoHubba in cytoscape software, the hub genes were found out. To verify the expression levels of hub genes, Gene Expression Profiling Interactive Analysis (GEPIA) was performed. Last but not least, UALCAN analysis online tool was implemented to analyze the overall survival.Results: The 376 DEGs were highly enriched in biological processes including signal transduction, apoptotic process and several pathways, mainly associated with Protein digestion and absorption and Pancreatic secretion pathway. The expression levels of nucleolar and spindle associated protein 1 (NUSAP1) and SHC binding and spindle associated 1 (SHCBP1) were discovered highly expressed in pancreatic ductal adenocarcinoma tissues. NUSAP1 and SHCBP1 had a high correlation with prognosis.Conclusions: The findings of this bioinformatics analysis indicate that NUSAP1 and SHCBP1 may be key factors in the prognosis and treatment of pancreatic cancer.

Download Full-text