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Kordshouli SO, Tahmasebi A, Moghadam A, Ramezani A, Niazi A. A comprehensive meta-analysis of transcriptome data to identify signature genes associated with pancreatic ductal adenocarcinoma. PLoS One 2024; 19:e0289561. [PMID: 38324544 PMCID: PMC10849254 DOI: 10.1371/journal.pone.0289561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/20/2023] [Indexed: 02/09/2024] Open
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) has a five-year survival rate of less than 5%. Absence of symptoms at primary tumor stages, as well as high aggressiveness of the tumor can lead to high mortality in cancer patients. Most patients are recognized at the advanced or metastatic stage without surgical symptom, because of the lack of reliable early diagnostic biomarkers. The objective of this work was to identify potential cancer biomarkers by integrating transcriptome data. METHODS Several transcriptomic datasets comprising of 11 microarrays were retrieved from the GEO database. After pre-processing, a meta-analysis was applied to identify differentially expressed genes (DEGs) between tumor and nontumor samples for datasets. Next, co-expression analysis, functional enrichment and survival analyses were used to determine the functional properties of DEGs and identify potential prognostic biomarkers. In addition, some regulatory factors involved in PDAC including transcription factors (TFs), protein kinases (PKs), and miRNAs were identified. RESULTS After applying meta-analysis, 1074 DEGs including 539 down- and 535 up-regulated genes were identified. Pathway enrichment analyzes using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that DEGs were significantly enriched in the HIF-1 signaling pathway and focal adhesion. The results also showed that some of the DEGs were assigned to TFs that belonged to 23 conserved families. Sixty-four PKs were identified among the DEGs that showed the CAMK family was the most abundant group. Moreover, investigation of corresponding upstream regions of DEGs identified 11 conserved sequence motifs. Furthermore, weighted gene co-expression network analysis (WGCNA) identified 8 modules, more of them were significantly enriched in Ras signaling, p53 signaling, MAPK signaling pathways. In addition, several hubs in modules were identified, including EMP1, EVL, ELP5, DEF8, MTERF4, GLUP1, CAPN1, IGF1R, HSD17B14, TOM1L2 and RAB11FIP3. According to survival analysis, it was identified that the expression levels of two genes, EMP1 and RAB11FIP3 are related to prognosis. CONCLUSION We identified several genes critical for PDAC based on meta-analysis and system biology approach. These genes may serve as potential targets for the treatment and prognosis of PDAC.
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Affiliation(s)
| | | | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Amin Ramezani
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
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2
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Lin CH, Hsu TI, Chiou PY, Hsiao M, Wang WC, Chen YC, Lin JT, Wang JY, Lin PC, Lin FC, Tseng YK, Cheng HC, Chen CL, Lu PJ. Downregulation of STK4 promotes colon cancer invasion/migration through blocking β-catenin degradation. Mol Oncol 2020; 14:2574-2588. [PMID: 32741119 PMCID: PMC7530774 DOI: 10.1002/1878-0261.12771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/13/2020] [Accepted: 07/27/2020] [Indexed: 01/03/2023] Open
Abstract
Mammalian STE20-like kinase 1 (MST1/STK4/KRS2) encodes a serine/threonine kinase that is the mammalian homolog of Drosophila Hippo. STK4 plays an important role in controlling cell growth, apoptosis, and organ size. STK4 has been studied in many cancers with previous studies indicating an involvement in colon cancer lymph node metastasis and highlighting its potential as a diagnostic marker for colon cancer. However, the role of STK4 defect in promoting colon cancer progression is still understudied. Here, we found that STK4 was significantly downregulated in colon cancer and was associated with distal metastasis and poor survival. Furthermore, STK4 knockdown enhanced sphere formation and metastasis in vitro and promoted tumor development in vivo. We found that STK4 colocalized with β-catenin and directly phosphorylated β-catenin resulting in its degradation via the ubiquitin-mediated pathway. This may suggest that STK4 knockdown causes β-catenin phosphorylation failure and subsequently β-catenin accumulation, consequently leading to anchorage-independent growth and metastasis in colon cancer. Our results support that STK4 may act as a potential candidate for the assessment of β-catenin-mediated colon cancer prognosis.
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Affiliation(s)
- Cheng-Han Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tai-I Hsu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Yu Chiou
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Ching Wang
- Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan
| | - Yu-Chia Chen
- Division of General Surgery, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Jen-Tai Lin
- Division of Urology, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Jaw-Yuan Wang
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Surgery, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung, Taiwan
| | - Peng-Chan Lin
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Forn-Chia Lin
- Department of Radiation Oncology, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Kai Tseng
- Department of Orthopedics, Show Chwan Memorial Hospital, Changhua, Taiwan.,Department of Orthopedics, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Hui-Chuan Cheng
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Long Chen
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Pathology, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Pei-Jung Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Clinical Medicine Research Center, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
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3
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The role of long non-coding RNA AFAP1-AS1 in human malignant tumors. Pathol Res Pract 2018; 214:1524-1531. [PMID: 30173945 DOI: 10.1016/j.prp.2018.08.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/06/2018] [Accepted: 08/18/2018] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Long non-coding RNAs (lncRNAs) are a type Table of endogenous RNA longer than 200 nucleotides in length, and this kind of RNAs lack or possess limited ability of coding proteins. A large number of studies have demonstrated that lncRNAs could take part in massive biological processes, such as transcriptional activation and interference, cellular differentiation, proliferation, migration, invasion and apoptosis. The abnormal expression of lncRNAs has been clarified to play extremely important roles in various diseases, especially in human cancers. LncRNA actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1) is a newly recognized cancer-related lncRNA deriving from the antisense strand of DNA at the AFAP1 coding gene locus. A slew of new studies suggest that AFAP1-AS1 is involved in many kinds of malignant tumors. Moreover, in recent years, the dysregulated expression of AFAP1-AS1 has been confirmed to be associated with oncogenesis and tumor progression. Evidence has increasingly shown that AFAP1-AS1 could probably serve as a novel potential molecular biomarker in tumor diagnosis and therapeutic target in tumor treatment. In this review, we sum up present stage new hottest research issues in respect of the biological functions and molecular mechanisms of AFAP1-AS1 in occurrence and progression of human tumors. MATERIALS AND METHODS In this review, we summarize the recent researches about the expression and molecular biological mechanisms of lncRNA AFAP1-AS1 in tumor development. Existing relevant studies are acquired and analyzed by searching Pubmed, BioMedNet, GEO database and Academic Search Elit systematically. RESULTS Long non-coding RNA AFAP1-AS1 is an important tumor-associated lncRNA and its aberrant expression has been found in many malignancies so far, including pancreatic ductal adenocarcinoma, cholangiocarcinoma, gallbladder cancer, hepatocellular carcinoma, gastric cancer, colorectal cancer, esophageal cancer, nasopharyngeal carcinoma, lung cancer, ovarian cancer, breast cancer, retinoblastoma, laryngeal cancer, tongue squamous cell carcinoma and thyroid cancer. In addition, the dysregulated expression of AFAP1-AS1 is related to carcinogensis, overall survival (OS), disease-free survival (DFS), progression-free survival (PFS) and tumor progression containing lymph node metastasis, distant metastasis, histological grade, tumor size and tumor stage. CONCLUSIONS A series of studies provide detailed information to understand lncRNA AFAP1-AS1 role in various human cancers. LncRNA AFAP1-AS1 is an oncogene in tumors that have been studied so far, and it may act as a useful tumor biomarker and therapeutic target.
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Dissection of Protein Kinase Pathways in Live Cells Using Photoluminescent Probes: Surveillance or Interrogation? CHEMOSENSORS 2018. [DOI: 10.3390/chemosensors6020019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Identification of MST1 as a potential early detection biomarker for colorectal cancer through a proteomic approach. Sci Rep 2017; 7:14265. [PMID: 29079854 PMCID: PMC5660227 DOI: 10.1038/s41598-017-14539-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 10/12/2017] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is a common malignant neoplasm worldwide. It is important to identify new biomarkers for the early detection of CRC. In this study, magnetic beads and the Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) platform were used to analyse CRC and healthy control (HC) serum samples. The CRC diagnosis pattern was established to have a specificity of 94.7% and sensitivity of 92.3% in a blind test. The candidate biomarker serine/threonine kinase 4 (STK4, also known as MST1) was identified by Tandem mass spectrometry (MS/MS) and verified with western blotting and enzyme-linked immunosorbent assay (ELISA). The results indicated that there was a higher concentration of MST1 in HC subjects than stage I CRC patients for the early detection of CRC and a lower concentration in stage IV patients than in other CRC patients. The sensitivity and specificity of MST1 combined with carcinoembryonic antigen (CEA) and faecal occult blood test (FOBT) in diagnosis of colorectal cancer were 92.3% and 100%, respectively. Additionally, low MST1 expression was associated with the poor prognosis. These results illustrate that MST1 is a potential biomarker for early detection, prognosis and prediction of distant metastasis of CRC.
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Kuppusamy P, Govindan N, Yusoff MM, Ichwan SJ. Proteins are potent biomarkers to detect colon cancer progression. Saudi J Biol Sci 2017; 24:1212-1221. [PMID: 28855814 PMCID: PMC5562385 DOI: 10.1016/j.sjbs.2014.09.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 09/21/2014] [Accepted: 09/24/2014] [Indexed: 01/11/2023] Open
Abstract
Colon cancer is the most common type of cancer and major cause of death worldwide. The detection of colon cancer is difficult in early stages. However, the secretory proteins have been used as ideal biomarker for the detection of colon cancer progress in cancer patients. Serum/tissue protein expression could help general practitioners to identify colon cancer at earlier stages. By this way, we use the biomarkers to evaluate the anticancer drugs and their response to therapy in cancer models. Recently, the biomarker discovery is important in cancer biology and disease management. Also, many measurable specific molecular components have been studied in colon cancer therapeutics. The biomolecules are mainly DNA, RNA, metabolites, enzymes, mRNA, aptamers and proteins. Thus, in this review we demonstrate the important protein biomarker in colon cancer development and molecular identification of protein biomarker discovery.
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Affiliation(s)
- Palaniselvam Kuppusamy
- Mammalian Cell Technology Laboratory, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Natanamurugaraj Govindan
- Mammalian Cell Technology Laboratory, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Mashitah M. Yusoff
- Mammalian Cell Technology Laboratory, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Solachuddin J.A. Ichwan
- Kulliyyah of Dentistry, International Islamic University Malaysia, Bandar Indera Mahkota 125200, Kuantan, Pahang, Malaysia
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Wang H, Luo C, Zhu S, Fang H, Gao Q, Ge S, Qu H, Ma Q, Ren H, Wang Y, Wang W. Serum peptidome profiling for the diagnosis of colorectal cancer: discovery and validation in two independent cohorts. Oncotarget 2017; 8:59376-59386. [PMID: 28938643 PMCID: PMC5601739 DOI: 10.18632/oncotarget.19587] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/29/2017] [Indexed: 01/05/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant neoplasms worldwide. Except for the existing fecal occult blood test, colonoscopy and sigmoidoscopy, no widely accepted in vitro diagnostic methods have been available. To identify potential peptide biomarkers for CRC, serum samples from a discovery cohort (100 CRC patients and 100 healthy controls) and an independent validation cohort (91 CRC patients and 91 healthy controls) were collected. Peptides were fractionated by weak cation exchange magnetic beads (MB-WCX) and analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Five peptides (peaks at m/z 1895.3, 2020.9, 2080.7, 2656.8 and 3238.5) were identified as candidate biomarkers for CRC. A diagnostic panel based on the five peptides can discriminate CRC patients from healthy controls, with an accuracy of 91.8%, sensitivity of 95.6%, and specificity of 87.9% in the validation cohort. Peptide peaks at m/z 1895.3, 2020.9 and 3238.5 were identified as the partial sequences of complement component 4 (C4), complement component 3 (C3) and fibrinogen α chain (FGA), respectively. This study potentiated peptidomic analysis as a promising in vitro diagnostic tool for diagnosis of CRC. The identified peptides suggest the involvement of the C3, C4 and FGA in CRC pathogenesis.
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Affiliation(s)
- Hao Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Chenghua Luo
- Department of Retroperitoneal Tumors Surgery, Peking University International Hospital, Beijing 102206, China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100069, China.,National Center for Clinical Medical Research of Digestive Diseases, Beijing 100069, China
| | - Honghong Fang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Qing Gao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Siqi Ge
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.,School of Medical and Health Sciences, Edith Cowan University, Perth 6027, Australia
| | - Haixia Qu
- Bioyong (Beijing) Technology Co., Ltd., Beijing 100085, China
| | - Qingwei Ma
- Bioyong (Beijing) Technology Co., Ltd., Beijing 100085, China
| | - Hongwei Ren
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Wei Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.,School of Medical and Health Sciences, Edith Cowan University, Perth 6027, Australia
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Moreira FTC, Ferreira MJMS, Puga JRT, Sales MGF. Screen-printed electrode produced by printed-circuit board technology. Application to Cancer Biomarker Detection by means of plastic antibody as sensing material. SENSORS AND ACTUATORS. B, CHEMICAL 2016; 223:927-935. [PMID: 30740000 PMCID: PMC6366552 DOI: 10.1016/j.snb.2015.09.157] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This research work presents, for the first time, a screen-printed electrode (SPE) made on a PCB board with silver tracks (Ag) and a three electrode configuration (AgxO-working, AgxO-counter and Ag/AgxO-reference electrodes), following the same approach as printed-circuit boards (PCBs). This low cost and disposable device was tested for screening a cancer biomarker in point-of-care. The selected biomarker was carcinogenic embryonic antigen (CEA) protein, routinely used to follow-up the progression of specific cancer diseases. The biosensor was constructed by assembling a plastic antibody on the Ag-working electrode area, acting as the biorecognition element of the device. The protein molecules that were entrapped on the polymer and positioned at the outer surface of the polypyrrole (PPy) film were removed by protease action. The imprinting effect was tested by preparing non-imprinted (NPPy) material, including only PPy as biorecognition element. Infrared and Raman studies confirmed the surface modification of these electrodes. The ability of the sensing material to rebind CEA was measured by several electrochemical techniques: cyclic voltammetry (CV), impedance spectroscopy (EIS) and square wave voltammetry (SWV). The linear response ranged from 0.05 to 1.25 pg/mL against logarithm concentration. Overall, producing screen-printed electrodes by means of conventional PCB technology showed promising features, mostly regarding cost and prompt availability. The plastic antibody-based biosensor also seems to be a promising tool for screening CEA in point-of-care, with low response time, low cost, good sensitivity and high stability.
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Affiliation(s)
- Felismina T C Moreira
- BioMark-CINTESIS/ISEP, School of Engineering, Polytechnic Institute of Porto, Portugal
| | | | - José R T Puga
- TID-CINTESIS/ School of Engineering, Polytechnic Institute of Porto, Portugal
| | - M Goreti F Sales
- BioMark-CINTESIS/ISEP, School of Engineering, Polytechnic Institute of Porto, Portugal
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Li W, Xiao J, Zhou X, Xu M, Hu C, Xu X, Lu Y, Liu C, Xue S, Nie L, Zhang H, Li Z, Zhang Y, Ji F, Hui L, Tao W, Wei B, Wang H. STK4 regulates TLR pathways and protects against chronic inflammation-related hepatocellular carcinoma. J Clin Invest 2015; 125:4239-54. [PMID: 26457732 DOI: 10.1172/jci81203] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 08/28/2015] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is frequently associated with pathogen infection-induced chronic inflammation. Large numbers of innate immune cells are present in HCCs and can influence disease outcome. Here, we demonstrated that the tumor suppressor serine/threonine-protein kinase 4 (STK4) differentially regulates TLR3/4/9-mediated inflammatory responses in macrophages and thereby is protective against chronic inflammation-associated HCC. STK4 dampened TLR4/9-induced proinflammatory cytokine secretion but enhanced TLR3/4-triggered IFN-β production via binding to and phosphorylating IL-1 receptor-associated kinase 1 (IRAK1), leading to IRAK1 degradation. Notably, macrophage-specific Stk4 deletion resulted in chronic inflammation, liver fibrosis, and HCC in mice treated with a combination of diethylnitrosamine (DEN) and CCl4, along with either LPS or E. coli infection. STK4 expression was markedly reduced in macrophages isolated from human HCC patients and was inversely associated with the levels of IRAK1, IL-6, and phospho-p65 or phospho-STAT3. Moreover, serum STK4 levels were specifically decreased in HCC patients with high levels of IL-6. In STK4-deficient mice, treatment with an IRAK1/4 inhibitor after DEN administration reduced serum IL-6 levels and liver tumor numbers to levels similar to those observed in the control mice. Together, our results suggest that STK4 has potential as a diagnostic biomarker and therapeutic target for inflammation-induced HCC.
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MESH Headings
- Animals
- Carbon Tetrachloride/toxicity
- Carcinoma, Hepatocellular/chemistry
- Carcinoma, Hepatocellular/etiology
- Carcinoma, Hepatocellular/immunology
- Cytokines/metabolism
- Diethylnitrosamine
- Escherichia coli Infections/complications
- Female
- HEK293 Cells
- Hepatitis, Animal/chemically induced
- Hepatitis, Animal/immunology
- Humans
- Immunity, Innate
- Interferon-beta/biosynthesis
- Interferon-beta/genetics
- Interleukin-1 Receptor-Associated Kinases/physiology
- Interleukin-6/analysis
- Intracellular Signaling Peptides and Proteins
- Lipopolysaccharides/toxicity
- Liver Neoplasms/chemistry
- Liver Neoplasms/etiology
- Liver Neoplasms/immunology
- Liver Neoplasms, Experimental/etiology
- Liver Neoplasms, Experimental/genetics
- Liver Neoplasms, Experimental/immunology
- Liver Neoplasms, Experimental/prevention & control
- Lung/immunology
- Lung/pathology
- Macrophages/immunology
- Macrophages/metabolism
- Male
- Mice
- Neoplasm Proteins/analysis
- Phosphorylation
- Protein Processing, Post-Translational
- Protein Serine-Threonine Kinases/blood
- Protein Serine-Threonine Kinases/deficiency
- Protein Serine-Threonine Kinases/physiology
- STAT3 Transcription Factor/analysis
- Signal Transduction
- Specific Pathogen-Free Organisms
- Toll-Like Receptors/immunology
- Transcription Factor RelA/analysis
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Liu YJ, Zhang S, Hou K, Li YT, Liu Z, Ren HL, Luo D, Li SH. Analysis of key genes and pathways associated with colorectal cancer with microarray technology. Asian Pac J Cancer Prev 2014; 14:1819-23. [PMID: 23679280 DOI: 10.7314/apjcp.2013.14.3.1819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Microarray data were analyzed to explore key genes and their functions in progression of colorectal cancer (CRC). METHODS Two microarray data sets were downloaded from Gene Expression Omnibus (GEO) database and differentially expressed genes (DEGs) were identified using corresponding packages of R. Functional enrichment analysis was performed with DAVID tools to uncover their biological functions. RESULTS 631 and 590 DEGs were obtained from the two data sets, respectively. A total of 32 common DEGs were then screened out with the rank product method. The significantly enriched GO terms included inflammatory response, response to wounding and response to drugs. Two interleukin-related domains were revealed in the domain analysis. KEGG pathway enrichment analysis showed that the PPAR signaling pathway and the renin-angiotensin system were enriched in the DEGs. CONCLUSIONS Our study to systemically characterize gene expression changes in CRC with microarray technology revealed changes in a range of key genes, pathways and function modules. Their utility in diagnosis and treatment now require exploration.
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Affiliation(s)
- Yan-Jun Liu
- Department of General Surgery, The Third People's Hospital of Chengdu, The Second Clinical College Affiliated to Chongqing Medical University, Chengdu, Sichuan, China
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