Integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinoma

Abstract Background Pancreatic duct adenocarcinoma (PDAC) remains a major health problem because conventional cancer treatments are relatively ineffective against it. Microarray studies have linked many genes to pancreatic cancer, but the available data have not been extensively mined for potential...

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Main Authors: Jun Li, Wenle Tan, Linna Peng, Jialiang Zhang, Xudong Huang, Qionghua Cui, Jian Zheng, Wen Tan, Chen Wu, Dongxin Lin
Format: Article
Language:English
Published: Wiley 2018-04-01
Series:Cancer Communications
Subjects:
GEO
Online Access:http://link.springer.com/article/10.1186/s40880-018-0289-9
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spelling doaj-80023d75d0024d36a3381ed7229e518d2020-11-25T04:02:00ZengWileyCancer Communications2523-35482018-04-0138111210.1186/s40880-018-0289-9Integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinomaJun Li0Wenle Tan1Linna Peng2Jialiang Zhang3Xudong Huang4Qionghua Cui5Jian Zheng6Wen Tan7Chen Wu8Dongxin Lin9Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeDepartment of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeDepartment of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeSun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineDepartment of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeDepartment of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeSun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineDepartment of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeDepartment of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeDepartment of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeAbstract Background Pancreatic duct adenocarcinoma (PDAC) remains a major health problem because conventional cancer treatments are relatively ineffective against it. Microarray studies have linked many genes to pancreatic cancer, but the available data have not been extensively mined for potential insights into PDAC. This study attempted to identify PDAC-associated genes and signaling pathways based on six microarray-based profiles of gene expression in pancreatic cancer deposited in the gene expression omnibus database. Methods Pathway network methods were used to analyze core pathways in six publicly available pancreatic cancer gene (GSE71989, GSE15471, GSE16515, GSE32676, GSE41368 and GSE28735) expression profiles. Genes potentially linked to PDAC were assessed for potential impact on survival time based on data in The Cancer Genome Atlas and International Cancer Genome Consortium databases, and the expression of one candidate gene (CKS2) and its association with survival was examined in 102 patients with PDAC from our hospital. Effects of CKS2 knockdown were explored in the PDAC cell lines BxPC-3 and CFPAC-1. Results The KEGG signaling pathway called “pathway in cancer” may play an important role in pancreatic cancer development and progression. Five genes (BIRC5, CKS2, ITGA3, ITGA6 and RALA) in this pathway were significantly associated with survival time in patients with PDAC. CKS2 was overexpressed in PDAC samples from our hospital, and higher CKS2 expression in these patients was associated with shorter survival time. CKS2 knockdown substantially inhibited PDAC cell proliferation in vitro. Conclusions Analysis integrating existing microarray datasets allowed identification of the “pathway in cancer” as an important signaling pathway in PDAC. This integrative approach may be powerful for identifying genes and pathways involved in cancer.http://link.springer.com/article/10.1186/s40880-018-0289-9Pancreatic cancerGEOPathway networkCKS2
collection DOAJ
language English
format Article
sources DOAJ
author Jun Li
Wenle Tan
Linna Peng
Jialiang Zhang
Xudong Huang
Qionghua Cui
Jian Zheng
Wen Tan
Chen Wu
Dongxin Lin
spellingShingle Jun Li
Wenle Tan
Linna Peng
Jialiang Zhang
Xudong Huang
Qionghua Cui
Jian Zheng
Wen Tan
Chen Wu
Dongxin Lin
Integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinoma
Cancer Communications
Pancreatic cancer
GEO
Pathway network
CKS2
author_facet Jun Li
Wenle Tan
Linna Peng
Jialiang Zhang
Xudong Huang
Qionghua Cui
Jian Zheng
Wen Tan
Chen Wu
Dongxin Lin
author_sort Jun Li
title Integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinoma
title_short Integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinoma
title_full Integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinoma
title_fullStr Integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinoma
title_full_unstemmed Integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinoma
title_sort integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinoma
publisher Wiley
series Cancer Communications
issn 2523-3548
publishDate 2018-04-01
description Abstract Background Pancreatic duct adenocarcinoma (PDAC) remains a major health problem because conventional cancer treatments are relatively ineffective against it. Microarray studies have linked many genes to pancreatic cancer, but the available data have not been extensively mined for potential insights into PDAC. This study attempted to identify PDAC-associated genes and signaling pathways based on six microarray-based profiles of gene expression in pancreatic cancer deposited in the gene expression omnibus database. Methods Pathway network methods were used to analyze core pathways in six publicly available pancreatic cancer gene (GSE71989, GSE15471, GSE16515, GSE32676, GSE41368 and GSE28735) expression profiles. Genes potentially linked to PDAC were assessed for potential impact on survival time based on data in The Cancer Genome Atlas and International Cancer Genome Consortium databases, and the expression of one candidate gene (CKS2) and its association with survival was examined in 102 patients with PDAC from our hospital. Effects of CKS2 knockdown were explored in the PDAC cell lines BxPC-3 and CFPAC-1. Results The KEGG signaling pathway called “pathway in cancer” may play an important role in pancreatic cancer development and progression. Five genes (BIRC5, CKS2, ITGA3, ITGA6 and RALA) in this pathway were significantly associated with survival time in patients with PDAC. CKS2 was overexpressed in PDAC samples from our hospital, and higher CKS2 expression in these patients was associated with shorter survival time. CKS2 knockdown substantially inhibited PDAC cell proliferation in vitro. Conclusions Analysis integrating existing microarray datasets allowed identification of the “pathway in cancer” as an important signaling pathway in PDAC. This integrative approach may be powerful for identifying genes and pathways involved in cancer.
topic Pancreatic cancer
GEO
Pathway network
CKS2
url http://link.springer.com/article/10.1186/s40880-018-0289-9
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